- 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 Lander One sets down, it lands 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, 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.
- 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.
- 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.
- 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.
- 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.
- When Daniels and Tennessee open the terraforming bay doors to eject the Xenomorph from the Covenant, the ejected trucks fall planetward, 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.
- 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.