The numerous mistakes and plot holes in Alien: Colonial Marines, especially with regards to continuity with the films that preceded it, were much criticized upon the game's release, especially given Gearbox Software's repeated assurances during development that the game would honor and fit into the continuity of the film series. It should be noted that some of the main game's plot holes were later explained in its singleplayer expansion pack Stasis Interrupted; issues addressed in this fashion are noted below. However, the removal of these key plot details from the base game seems dubious at best. Regardless, many of the game's plot holes are not clarified in this manner, while Stasis Interrupted additionally introduced further continuity problems and plot holes to the story.
- Before the game, the Sulaco was last seen passing Fiorina "Fury" 161 on its way back to its home base (presumably Earth) at the beginning of Alien3, yet in the game it is suddenly back at LV-426; this discrepancy is even brought up by Lieutenant Reid at the beginning of the game, before being quickly put aside by Captain Cruz. Moreover, the Sulaco is completely infested with Xenomorphs in the game. While it is implied that the location and condition of the ship are the result of interference by Weyland-Yutani personnel, who have taken over the vessel, this is never convincingly explained or elaborated upon. The reason for this infestation, as well as the ship's return to LV-426, were later explained in Stasis Interrupted.
- The various underbarrel weapon attachments in the game are never reloaded; any additional ammunition collected for them is magically teleported inside the weapons.
- Spare magazines for the 88 Mod 4 Combat Pistol that are found lying around levels and used when reloading contain white-colored 9mm rounds, yet when firing the weapon the casings that are ejected are bronze in color.
- The Sulaco's hangar is drastically smaller that it was in the film, and there is clearly no room for the second dropship. The hangar set used in the filming of Aliens was actually extended with a matte painting, and it appears the development team at Gearbox Software overlooked this in the set blueprints they used for reference (although a cursory look at the film would show the hangar's immense size).
- Bishop's legs are found on the floor in the Sulaco's hangar bay, even though they should logically have been sucked out of the vessel when Ripley opened the airlock to expel the Queen. The position they are found also does not correspond to events of the film — in Aliens, Bishop is standing behind Smart Ass when he is ripped in two and his legs are flung rewards with regards to the dropship, yet in the game his legs are found in front of the craft.
- There are multiple errors with the lockers in the Sulaco's locker room. For example, Tim Crowe's name is incorrectly displayed as "S. Crow" on his locker name plate. The door on Hicks' locker also opens to the wrong side when compared to Aliens, and the photographs visible inside in the film are missing.
- There are only twelve cryotubes in the Sulaco's hypersleep bay, even though there were fifteen people — twelve Marines plus Ripley, Burke and Bishop — on the ship in Aliens. This is actually accurate to the film, as the production could only afford to build six capsules and simply gave the illusion of more through the use of a large mirror that doubled the length of the room (and the number of cryotubes present). However, whereas selective camera angles hid the true number of pods in the film, in the game it is obvious there are not enough for the fifteen crew.
- There is little to no fire damage inside the hypersleep bay on the Sulaco, even though in Alien3 we see the entire chamber apparently being engulfed in flames.
- Additionally, the location of the missing cryotubes (the ones that were ejected with Ripley and co. inside at the start of Alien3) is wrong. In the game, they are at the right-hand end of the line of cryotubes (when looking at them from the center of the room). In Aliens, Ripley and the others go to sleep at the left-hand end of the bank of chambers, as the adjacent wall there is visible close in the background.
- Once again, Chestburster implantation has been rapidly accelerated. Keyes is discovered almost immediately after his squad is decimated by the Xenomorphs, yet he has already been cocooned and impregnated. Bella is also impregnated in far less than the 24 hours the process should take. In one of the audio logs discovered in the game, a Weyland-Yutani scientist claims the implantation process takes "roughly an hour or so", but even this seems far longer than it takes with Keyes and Bella.
- When Bella contacts her comrades for the first time, she clearly states her name. O'Neal then makes the nonsensical statement, "That sounded like Bella."
- When the USS Sephora arrives at LV-426, it is facing in the opposite direction to the Sulaco. However, when looking out from the Sulaco's windows whilst moving through the ship, you can see that the Sephora has suddenly turned 180° and is now facing in the same direction as her sister ship.
- Cruz refers to Ellen Ripley as a Warrant Officer we he summarizes the events of Aliens, yet by the time of the mission to LV-426 she actually held the rank of Lieutenant 1st Class.
- One of the major locations in the game is the colony of Hadley's Hope, despite the fact this location was supposedly completely obliterated by the detonation of its Atmosphere Processing Plant in Aliens. According to Bishop in the film, this explosion would have vaporized everything within a 30 km radius, yet in the game, even the Atmosphere Processor itself has not been obliterated, as a large portion of it is still standing. The colony is also somehow still present, despite the Processing station being, at most, four or five kilometers away; while the buildings have been superficially damaged, many of its structures are essentially intact.
- Furthermore, the design of Hadley's Hope does not match what we see in the films. For example, the colony has a storm wall completely encircling it in the game, whereas in the film it has a wall only on one side (as the moon's winds only ever come from one direction).
- When Corporal Winter and the others first arrive at the colony, there is an APC parked outside the perimeter wall. This can only be the APC from Aliens, yet in the film the APC was destroyed by the crashing dropship, and this happened close to the Atmosphere Processing Plant, some distance from the colony.
- The Operations Center interior shows no sign of the blast damage that would have been caused caused by Private Vasquez firing several grenades from her Pulse Rifle inside the room; even the glass monitor screens are intact. The vent that the survivors flee through following the assault in Aliens is also nowhere to be seen in the game.
- There are multiple errors regarding the two robot sentry guns found outside Operations (a reference to the Special Edition of Aliens):
- Neither of the guns is in the position it was in in the film — in Aliens, they were placed at a junction in the corridors near the main door into Operations, but in the game they are found in the middle of a corridor behind the med lab. The guns are also missing their battery/computer control packs, which in the film had to be wired into the guns separately in order for them to work.
- Both guns, like all of the sentry guns seen in the game, have prominent LCD ammunition counters, but the weapons in the film did not have these. According to these counters, one of the guns is empty, while the other has only 4 rounds remaining — while this is partially accurate to the film, the last gun in Aliens actually had 10 rounds remaining when it ceased firing. While it could be argued an errant Xenomorph may have strayed in front of it at some point between the events of the film and the game, causing it to fire the 6 missing rounds, the gun will not fire when the area is later attacked by Xenomorphs, even if one of the creatures stands directly in front of it.
- The gun with ammunition remaining has a two-digit ammo counter, even though every other sentry gun encountered in the game — including the one sitting directly alongside it — has a three-digit counter.
- When Winter and Private O'Neal first encounter the guns, Winter says, "Guns are dry. Every last bullet," despite the fact one of the guns clearly shows 4 rounds remaining on its ammunition counter.
- When the Xenomorphs launch their first major assault on the Operations building, Cruz orders Winter to recover one of the sentry guns to help defend the area. The gun he picks up is empty, yet when he places it in Operations it suddenly has a full 500 round magazine without anyone reloading it.
- The doorway and window leading to the room where the Facehuggers are stored in the med lab has changed completely, as seen in the image to the right. The room itself is also different — the black stencilled writing on the wall is missing in the game and a metal support structure in its center has become a series of pipes. Finally, the six tubes containing Facehuggers are notably all full, despite the fact Bishop dissected one of the dead specimens and Burke released the two live creatures during Aliens.
- The two Facehuggers that were killed while attacking Ripley and Newt are in the wrong positions. The one killed by Hudson is trapped behind the small table – in the film it falls from the table and Hudson continues shooting it on the floor. The other Facehugger was thrown against a far wall by Hicks and shot dead there by Vasquez, but in the game it is lying near the middle of the room.
- The game gives Gorman's first name as William, both on his dog tag collectible and in the menu entry for Gorman's Pistol. However, in Aliens, the crew manifest seen on a monitor aboard the Sulaco gives Gorman's first initial as S. Alien: The Weyland-Yutani Report later clarified that his first name is indeed Scott.
- The head of Newt's doll Casey can be found in the sewers of Hadley's Hope. However, it is comically oversized compared to it's appearance in Aliens. It is also found atop a steel barrel, when in the film it is last seen sinking beneath the water in the flooded passage from which Newt is abducted.
- The design of the derelict on LV-426, like many other locations in the game, differs from what is seen in the films. Most notably, the circular platform on which the Pilot's chair sits in Alien — and which the Nostromo crew have to scale in order to investigate the lifeform — is absent. Also missing is the hole burned in the floor that led to the cargo hold.
- Despite his armor being destroyed by Xenomorph blood and abandoned inside Hadley's Hope in Aliens, Hicks is once again wearing his (undamaged) armor after he is rescued; it is not simply another set of armor that has been given to him by the Sephora Marines, as it is clearly marked with his name on the chest plate and features the heart and padlock motif from the film.
- Alien Resurrection establishes that when Ripley killed the Dragon and the Queen embryo on Fiorina 161, the Xenomorph species was effectively wiped out (at least to mankind's knowledge). This would mean the explosion at the end of Aliens had to have destroyed not only the Xenomorphs at Hadley's Hope, but the Derelict Ship and all of the Eggs on board it as well. This would of course make the events of Aliens: Colonial Marines impossible.
- The layout of the DLC weapon Ripley's Pulse Rifle is wrong — in Aliens, Ripley tapes the weapon together so that the flamethrower is on the left-hand side, closest to her body, and the Pulse Rifle is on the right-hand side. The two weapons are reversed in the game, with the Pulse Rifle closest to the player. The ammo counter on the M41A is also on the wrong side in the game, being on the left of the Pulse Rifle (although this is likely for gameplay reasons, to ensure it is visible to the player).
- Even though Hicks sends a distress call to the USCM, it somehow takes the USS Sephora 17 weeks to reach LV-426; in Aliens, Hicks explains that they can expect a rescue team to arrive after only 17 days, even without them sending a distress call. Stasis Interrupted later revealed that Hicks' distress call was not sent until much later than the main game would have you believe, and far closer to the point at which the Sephora arrives at the moon; while this might explain why it took the Sephora so long to get there, it raises the further question of why Hicks didn't send the message sooner.
- Regardless of when the distress call was sent, the game does not explain why the USCM did not send a search party sooner based solely on the fact that the Sulaco had disappeared. While it is conceivable Weyland-Yutani may have had a hand in delaying such an operation, especially given their own activities on the moon, this is never suggested or elaborated upon.
- If Weyland-Yutani are conducting highly illegal human and biological research aboard a hijacked USCM spacecraft, it makes no sense that every video camera, portable computer, cargo container, desk drawer and baseball cap on the Sulaco is emblazoned with their corporate logo, as O'Neal actually points out in the game. Similarly, all of the equipment and supplies at the Origin Facility — including many of the structures themselves — are likewise prominently marked with the company's logo.
- It is never explained why Weyland-Yutani decide to create and study a Hive aboard the Sulaco when they already have ample Xenomorph specimens and research facilities on LV-426. Nor is it explained why they return the Sulaco to LV-426, especially as this will only draw any USCM search team looking for it straight to the moon — and their top secret Origin Facility.
- In Alien3, Michael Bishop is desperate to recover Ripley and the embryonic Queen inside her from Fiorina 161. However, with the game's revelation that the company is already studying an abundance of Xenomorph specimens on LV-426, including a Queen, he has absolutely no need to do this.
- Bella quite clearly describes the aftermath of a Facehugger attack when she first contacts Winter and Cruz over the radio, yet no one shows any real concern until the Sephora's Bishop later informs her that she is impregnated and will soon die. Given that Ripley gave an account of the Alien and its life cycle when she was rescued from deep space in Aliens, it makes no sense that the Marines, and especially their commanding officer, would not realize Bella was in trouble immediately. The Marines in Aliens had read Ripley's report (even if they did not believe it until they encountered the Xenomorphs first-hand), so it is totally illogical that the detachment aboard the Sephora would be sent in without this information.
- Given that he was supposedly killed in Alien3, Hicks' survival and presence on LV-426 is completely unexplained in the main game. Stasis Interrupted would later divulge how he is still alive and what took place to convince Ripley and others he was killed on Fiorina 161, but the main game completely glosses over the situation.
- The game states Hicks is being held on LV-426 by Weyland-Yutani so that he can be tortured for information. However, he could not possibly know anything of any importance that the company has not already discovered for itself. Given the state of advancement of their operation, they know far more about the Xenomorphs than he ever did at this point.
- It seems strange that, given how Hicks had become close to Ripley by the end of Aliens (especially so in the extended Special Edition), he does not even think to ask what may have happened to her when he is rescued by the Sephora Marines. While dialogue in the game's ending implies that Hicks already knows of Ripley's death, it is never made clear exactly how he knows this. Stasis Interrupted later revealed that Hicks in fact witnessed Ripley's death first-hand.
- Towards the end of the game, Reid is repeatedly sent to do jobs that endanger her life, despite the fact she is apparently the last pilot the Marines have and therefore a vital lifeline to them. This would make sense if the survivors were critically short on manpower and had no alternative, but there are clearly enough Marines left alive for Reid to be kept safely away from the action and under guard.
- Magazines (for firearms) are incorrectly referred to as clips in-game.
- While the M41 series of Pulse Rifles use caseless ammunition, replacement magazines for the M41A MK2 seen when reloading in the game seem to contain traditional cased ammunition, judging by the metallic bronze color of the rounds. Moreover, the shape and dimensions of the individual cartridges are vastly different to the weapon's 10×24mm Caseless round as described in the Colonial Marines Technical Manual, which is actually rectangular in shape. However, despite this error, any spare M41A MK2 magazines found lying around the game's levels contain white rectangular-shaped rounds, closer to what is described in the Technical Manual.
- The Sephora's name is not painted on the vessel's hull, even though the area where it should be written is clearly visible as the player crosses the umbilical.
- The word "actual" is used incorrectly in radio communications repeatedly throughout the game. When referred to by others, unit commanders would be designated by their unit's callsign followed by the number 6; thus, Cruz would be Sephora-6 or Sulaco-6. The only time the word "actual" would be used in communications is to clarify that Cruz is the person actually speaking, and not his radio operator relaying the message.
- Bella has her first name written on her armor. This is contrary to military regulations — personnel would invariably have their last name given on any identifying badges, as is seen not only in Aliens, but on the armor of other Marines in the game itself. Furthermore, she is wearing earrings, which is likewise against military regulations and something no soldier would ever do.
- When reloading the M41A Pulse Rifle MK2 with either the U1 Grenade Launcher or U4 Firebomb Launcher attached, it is possible to see inside the underbarrel launchers, revealing them to be hollow.
- After Reid surveys the damage from the explosive decompression at the very beginning of the game, her dropship pulls up and away from the umbilical and passes straight through the Sephora's hull overhead.
- The expansion pack makes it definitively clear that Michael Weyland is intended to be the same character played by Lance Henriksen at the end of Alien3 (a fact hinted at but not confirmed in the main game). However, that character's name was actually Michael Bishop.
- Given that the DLC is set reasonably soon after the events of Alien3, Weyland should still be showing at least some sign of the grievous wound he suffered at the hands of Aaron on Fiorina 161, yet his head is not so much as scratched.
- There are a wealth of continuity errors in the scene that explains how Hicks is still alive:
- Hicks is wearing a T-shirt and pants when he is woken from hypersleep, yet at the end of Aliens he entered hypersleep in just his shorts. Additionally, the bandage that covered his left eye and a good portion of his face has mysteriously vanished in the game.
- We are expected to believe that Turk, the man who ends up inside Hicks' cryotube in his stead, arrived aboard the Sulaco semi-naked and wearing bandages in almost exactly the same places as the Corporal. While not outright impossible, this seems, at best, hugely unlikely.
- Hicks' dog tags are in the EEV when it crashes on Fiorina 161 — they are seen hanging on the door of the morgue refrigerator where his body is placed in Alien3, and are presumably how he was identified. However, in the game, Hicks is wearing his dog tags after the EEV launches without him. This would make it impossible for them to be on Fiorina.
- The Facehugger attached to Ripley is hit by a stray bullet fired by one of the Weyland-Yutani PMCs, yet she is not harmed in any way by its potent acid blood.
- The Facehugger on Ripley is also present when she is loaded into the EEV, yet a brief shot in the opening of Alien3 shows she does not have anything on her face at this point (even though, logically, she should).
- The huge fire that engulfs the hypersleep chamber in Alien3 (an incident confirmed by Bishop when Ripley reactivates him on Fiorina 161) never occurs in the game.
- Moreover, Bishop is able to determine from the Sulaco's flight recorder that there was a fire and a Facehugger on the ship, yet knows nothing of the USS Legato docking with the vessel, of Hicks being woken from hypersleep, of Weyland-Yutani soldiers storming the ship or of a firefight in the hypersleep bay.
- The computer voice aboard the Sulaco is completely different to that which is heard in Alien3 — it now speaks with an American accent, whereas in the film it was English.
- When Stone and Hicks raid the armory aboard the Sulaco for extra firepower, it is filled with M41A MK2s. Yet in Aliens the Marines carried the earlier M41A model; it would make no sense for those Marines to use older weaponry on their mission when newer stock was stored on the ship, therefore all the rifles in the armory should be the older model.
- During the recreation of the ending of Alien3, the distinctive Weyland-Yutani Commandos on Fiorina 161 are gone, replaced by the game's standard Weyland-Yutani PMCs. Morse is also not present on the gantry as he should be, and the mesh fence surrounding the spiral staircase up to the balcony where Weyland and his team are standing is likewise absent. Lastly, Weyland should be injured from Aaron's attack at this point, but the wound to his head is missing.
- When Hicks boards the EEV to escape the Resolute, his Pulse Rifle has a U7 Tac-Shotgun underbarrel attachment, yet at every other point (including during gameplay) it has standard U1 Grenade Launcher installed.
- In the level "Redemption", Levy twice has to don a gas mask and enter laboratories flooded with toxic gas. However, if you look at Levy's shadow on the wall, his gas mask is nowhere to be seen.
- The motion tracker that Lisbeth takes and uses aboard the Legato does not detect Andrews, Stone or Turk; while military operatives would likely be issued some kind of technology that prevents them from appearing on their own trackers, Andrews, Stone and Turk are civilians, and it seems improbable they would be outfitted with such equipment.
- PMCs aboard the Legato invariably spend several seconds screaming loudly when they are being subdued by Facehuggers, but this would be impossible if the creature is forcing its proboscis down their throats.