- 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.
- 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.
- 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.
- The Engineers depicted in Alien: Covenant look very dissimilar compared to the ones in Prometheus. Whether this design choice was intentional or not is yet to be seen.
- 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.
- 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.