- Between Aliens and this movie, the color of the Sulaco has changed from grey to brown, while the name on its hull is now written in white rather than black. The design of its hypersleep pods has also drastically changed, now appearing closer to those seen aboard the Nostromo in Alien.
- During the Sulaco evacuation sequence, a monitor shows an X-ray image of a Facehugger attached to someone. Later events tell us this must be Ripley, but there are several subsequent shots of Ripley during the opening that clearly show she has nothing on her face.
- Corporal Hicks' dog tags, which can be seen in the morgue, are of a different design to the ones seen in Aliens; in the previous film, they were clear plastic tags, but in Alien3, they are a more traditional metal design.
- In the extended Special Edition, the Facehugger that impregnates Ripley and Babe the ox is shown to be a larger Royal Facehugger, yet the creature glimpsed aboard the Sulaco during the opening credits is clearly a normal Facehugger, as it lacks the Royal Facehugger's distinctive webbing between its digits.
- The previous films establish that Facehuggers die as soon as they have implanted an embryo in their victim. However, the Facehugger in this film somehow impregnates two victims. The Special Edition explains this discrepancy by making the creature responsible a previously unseen Royal Facehugger, but this entire concept was scrapped from the theatrical version, making it seem as though a normal Facehugger is somehow suddenly capable of impregnating multiple hosts.
- In the mess hall, the amount of orange juice in Ripley's glass changes between shots.
- When Clemens is discussing the prison's history with Ripley in the assembly hall, he points out that it has been "reduced to a custodial staff of 25", implying there are 25 people in total at the facility (not including Ripley, who has only just arrived). However, when Ripley meets with Andrews in his office later, the Superintendent tells her that he has "25 prisoners in this facility", implying there must be at least 28 people on the planet (25 prisoners plus three members of staff). By considering all of the names mentioned in the film's shooting script, it seems there are actually 22 prisoners on Fiorina, plus three members of staff, making Clemens correct. It is possible, of course, that Andrews was metaphorically including himself, Aaron and Clemens in the prisoner count due to the fact they are effectively stuck running such a remote facility.
- In the theatrical version, the infant Dragon that comes out of Spike is bigger than the dog was to start with.
- In the Special Edition, Murphy still calls out for Spike when he notices the Dragon moving around in the hole in the side of the ventilation shaft, despite the fact his dog is otherwise removed from the extended cut of the movie.
- When Aaron radios Clemens in his quarters and tells him about Murphy's death, he tells him it happened in vent shaft 22. Later, when addressing the prisoners about the event, Andrews says it happened in vent shaft 17.
- In the Special Edition, the drinking bird on Andrews' desk is seen rocking back and forth when Clemens enters the room for their meeting, but when it is next seen it is completely stationary.
- The Dragon appears red-brown in shots using a physical suit, yet effects shots showing the rod-puppet creature often give it a greenish tint.
- Golic simply vanishes in the theatrical cut of the movie — he is last seen tied up in the infirmary during Clemens' death. The extended Special Edition features extra scenes with the character, revealing what happens to him, but his fate remains a mystery in the theatrical version of the film.
- Arthur is seen surveying the carnage after the explosion that kills many of the prisoners, yet a few moments later Morse and Dillon find his body.
- Dillon's glasses disappear during the conversation outside the nuclear waste tank after the plan to trap the Xenomorph fails in the theatrical version (or after it is released from the tank in the extended Special Edition). He puts them back on later in the scene, but we never see him take them off.
- In the Special Edition, David identifies the first person killed during the bait and chase sequence as Vincent. However, in the scenes immediately prior to this, all of the surviving prisoners can be identified, and none of them could be Vincent.
- When Dillon and Ripley back away from Kevin's dead body, it is some distance from the door where the Dragon is lurking, yet when the creature lunges in and snatches the corpse it is suddenly lying right in front of the doorway.
- Ripley is soaked in water when she douses the Dragon and causes it to explode, yet she is almost completely dry moments later when talking to Michael Bishop and his team. Even considering the high levels of heat inside the lead works, the change takes place far too quickly.
- In the previous Alien movies, the victims of Chestbursters have been completely incapacitated by pain during the "birth", yet when the infant Queen emerges from Ripley at the end of the theatrical cut she is quite serene, even calmly embracing the emerging Chestburster and hugging it against her body, displaying no evidence of pain or discomfort at all.
- Arguably one of the most notorious plot holes in movie history occurs right at the very beginning of the film — there is an Egg aboard the Sulaco, even though there is no conceivable way it could have gotten there. While it could be argued that the Queen brought it with her at the end of Aliens, a shot of her emerging from the elevator inside the Atmosphere Processing Plant in that film clearly shows she is not carrying anything with either of her two pairs of arms before getting on the dropship, and without her Egg sac, it seems unlikely she could lay one whilst on board. More confusingly, the Egg in Alien3 seems to be in a completely obscure part of the Sulaco, when the only place the Queen could reasonably have deposited one (had she brought one aboard) is somewhere within the dropship's undercarriage, before she attacked Bishop.
- The film never explains why the EEV crashes so catastrophically on Fiorina 161; after all, an escape pod would be of little use if it will simply slam into the nearest planet at high speed, killing most of the people on board. In the film's novelization, the pod is damaged by an explosion as it launches and this eventually leads to a cascade of system failures and the crash, but this explanation was cut from the film.
- When Clemens asks why they must perform an autopsy on Newt, Ripley tells him the girl may have contracted cholera, to which Clemens incredulously responds, "There hasn't been a case of cholera reported for 200 years." Even taking her extended hypersleep into account, this would mean cholera was eradicated over a century before Ripley was even born. It seems highly improbable she would suggest — or even know about — such a historical disease in the situation.
- At one point, Ripley mentions that the Xenomorphs she has encountered previously were afraid of fire. However, this was never really proven in the preceding films. In Alien, Ash proposes that the Alien may retreat from fire, but he is merely theorizing out loud when he says this. The only person to actually use a flamethrower in the vicinity of the Alien in the film is Dallas, and far from fleeing, the creature quickly captures him. In Aliens, Ripley sets fire to the Hive at the end of the film, but is still attacked by Xenomorphs while doing so. In fact, all evidence up to this point indicates fire has no greater effect on Xenomorphs than bullets — it is an effective weapon when used directly, but has no inherent intimidating impact on the creatures, and the mere threat of it is not enough to deter them. Alien: Isolation would later show that Xenomorphs are apparently afraid of fire to some degree, but it still stands that Ripley could not really know this in Alien3.
- At the end of the film, Ripley's signing off message from the end of Alien can be heard coming from the EEV, even though there is no reasonable way a recording of it could be stored on the pod. The novelization and comic adaptation of the film explain that the message is not actually stored in the EEV at all, but is in fact lingering in the radio waves of space and is simply being picked up by the battered radio equipment on board the EEV. However, the film never explains this, making it seem as if the recording is coming from the EEV itself, which makes no sense.
- When the EEV crashes into the ocean, a giant plume of water is thrown up. However, exterior shots of the planet show its surface is racked by ferocious winds, and as a result, the plume of water should have been blown immediately off to one side instead of rising neatly upwards.
- Ripley has a badly bloodshot eye following the EEV crash, yet it disappears quickly. Such an injury would actually take days to clear up.
- During the bait-and-chase sequence, Jude is heard screaming, "Help me!" as the Dragon chases him down a corridor. However, his face is clearly in view at the time and his lips are not moving.
- When Aaron attacks Bishop, he shouts out, "Fucking android!" However, the movement of his lips do not match his words.
- Space travel in the novelization of the third film suddenly takes vastly longer than it did in the preceding stories (and the film itself). In Aliens, the Sulaco takes two to three weeks to reach LV-426, but at the start of the Alien3 novelization it is stated that its return journey to Earth will take over two years. Likewise, Andrews at one point muses his friends and family will be dead by the time he returns home from Fiorina 161, due to the length of time spent traveling.