- When Walter is checking on the crew at the start of the film, Branson's serial number is given as 47532-385 on his cryo pod. At the end of the film, Tennessee's serial number is seen in the same fashion, yet the number given is the same as Branson's.
- When Walter removes the dead fetus from the storage tray near the beginning of the film, there is a small amount of blood left in the recess he takes it form. When he subsequently closes the tray, this blood is gone.
- When Ricks scans the system from which Shaw's transmission is emanating, he states that the fourth planet is orbiting in the habitable zone. However, the image on the monitor he is looking at highlights the third planet.
- Lander One sets down in shallow water that the crew have to wade through when they begin their expedition. Later, when the crew rush back to the dropship, the land surrounding it is dry. This would be entirely possible if the lake was tidal (something that is actually confirmed in the novelization), but when we see the dropship again before it explodes, it is surrounded by water once more, the change occurring far too quickly for it to be explained by tidal action.
- When Karine collects her first water sample, she closes the small plastic container before passing it to Ledward, who then closes it again.
- When she first radios the Covenant to inform the crew of Ledward's condition, Faris tells Tennessee that Karine reported Ledward was bleeding. However, Karine said no such thing when she radioed Faris earlier. Moreover, Ledward does not show any signs of bleeding until he vomits blood all over Karine's shoulder, and this happens after Faris has contacted the Covenant.
- After Faris gets sprayed with Ledward's blood, the amount of blood on her face varies from shot to shot and even disappears altogether when she is contacting her husband.
- Ledward's top is still partially covering his arms and back when the first Neomorph bursts from him, but when he tumbles backwards off the table his upper body is completely bare.
- Daniels' face gets splattered with blood but when she uses the radio to call the others, her face on the screen shows no blood. In the following shots the blood returns.
- During David's battle with Walter, he manages to disarm Walter of the knife he had, sending it flying offscreen. Walter then tackles David into a stone slab a distance away from where the knife dropped, however, the knife is suddenly shown to be within David's reach when next shown.
- When Daniels and Lopé flee the citadel, the sky overhead is clearly shown to be overcast with thick, roiling clouds. However, when Tennessee comes down in the cargo lift, he descends through clear skies over the plaza. Subsequently the thick cloud cover returns.
- After Daniels throws the beacon to guide Tennessee down, Lopé moves with his back to her and shoulders his rifle. In the next shot, he is suddenly holding his rifle down as he unslings his backpack, before shouldering his weapon once again.
- In Prometheus, it is established that synthetics like David do not breathe, yet before he runs to the cargo lift, he stands at the temple's entrance to look back, clearly out of breath.
- When David is masquerading as Walter at the end of the film, there is no wound visible under his chin (from when Daniels stabbed him with the nail hanging around her neck); the film previously established that David does not "heal" like Walter did, so this wound should be visible.
- Occasionally throughout the film, the beams from the security team's rifle laser sights are misaligned with the barrels of the guns.
- On the bridge of Lander One, the pilot's view through the forward windshield is almost completely blocked by several large computer monitors directly in front of them. This makes no sense from a design point of view.
- Faris' decision to set the lander down in water is unjustifiably risky. While she comments that the water is "smooth" and therefore likely shallow, she does not appear to have any real information as to how deep the edge of the lake is. Moreover, she does not know what obstructions might be hidden beneath the surface, nor whether the bottom is stable enough to support the lander's presumably considerable weight. Even assuming the landing is successful, there is the possibility that a sudden change in water level might swamp the lander at a later time (and both film and novel do indeed confirm the lake is tidal). Setting down where she does might be justified if the surrounding terrain was so uneven that there is literally no alternative, but moments after disembarking the crew are walking through a flat wheat field that would serve adequately as a landing site.
- The embryonic Facehuggers that David regurgitates and places into storage aboard the Covenant are contained within small ovoids that match those containing the human embryos already on board, to the point where they fit perfectly inside the recesses in storage tray. Yet David has never been on the Covenant before, and so he would have no way of knowing exactly where and how the human embryos are being stored in order to mimic the method for his Facehuggers.
- In the opening scene, the Covenant is damaged by a "neutrino storm". However, neutrinos are virtually massless particles that are so minute they typically pass through other matter without ever causing a reaction — they commonly pass though the entire Earth in such a fashion. With this in mind, they could not damage the ship as shown in the film.
- The atmospheric data shown when Ricks scans Planet 4 makes no sense. The figures seen on the screen give oxygen content as 29% and nitrogen content as 82%, but 29 + 82 is more than 100.
- When Walter asks MU-TH-UR to track the rogue transmission to its source, the computer gives the location in astronomical terms. However, it incorrectly uses the word "declension"; the correct term is "declination".
- Neanderthals are described as discovering music and then inventing culture. Neanderthals were actually a cousin species, and 98% of them were replaced by modern humans from Africa. Their culture was fixed and had no confirmed art, which began with modern humans.
- During the attack on Karine by the infant Neomorph, there is far more blood on the floor than what could possibly have come from Ledward or Karine.
- When Daniels and Tennessee eject the vehicles from the terraforming bay, there is seemingly nothing to propel them out beyond the force of the decompression. By the time Tennessee releases the second truck, the decompression has finished and the bay is now a complete vacuum, and thus there would be nothing to drag the vehicle out of the open airlock as shown.
- Moreover, the ejected trucks fall planetward after leaving the Covenant, which is factually incorrect — if the ship is in a stable orbit (as prior events imply), the ejected vehicles would not fall and would in fact likewise stay in orbit, at least until they lost significant velocity.
- The CGI Bloodburster is quite clearly unsynchronized with Karine when it attacks and mauls her in the med bay immediately following its birth; the creature rips and tears at her neck but she is holding a knife at a full arm's-length to defend herself as though the creature is a distance away and not directly on top of her.
- When Daniels is talking to the Covenant crew via laptop whilst sitting in the rain, her voice is audible but her mouth is visibly not moving.
- The book gives Shaw's year of birth as 2058, but according to Alien: The Weyland-Yutani Report she was born in 2061.
- When David is showing Oram around his lab, the dissected Engineer is first said to be lying on a table before later it is said to be standing upright.
- At one point, Daniels muses that Tennessee would never proceed with a risky plan without conferring with others, yet this is exactly what he tries to do when reducing the Covenant's orbit.
- While exploring the citadel, Walter discover's Shaw's living quarters. According to David, Shaw died in the Juggernaut crash, yet Walter never questions why she would have a room in the temple.
- During the scene where Sergeant Lopé is attacked by the Facehugger, the book specifically states that Lopé is able to get his arm between the creature and his face, blocking its ovipositor from entering his throat. This would therefore make it impossible for him to become impregnated.
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