Revealing mistakes

When David is pretending to be Walter at the end of the film, there is clearly no wound under his chin that was caused by Daniels when she stabbed him with a nail. David does not heal the same way that Walter does and the wound would have been recent enough to be visible.

Continuity

When Karine takes her first water sample, she syringes the water into a plastic container and then closes the lid. This sample is then handed to the marine who closes the lid again.

Plot holes

When David regurgitates the alien embryos and places them in the refrigerator with the human embryos, they are in exactly the same type of capsule and fit perfectly in the compartments. This is unlikely, given that David has been marooned for ten years and thus had no access to current technological advances.

Incorrectly regarded as goofs

At first glance it appears that when the Xenomorph climbs down the hole on the ship, its dorsal tubes phase through the floor. However they can be seen to be quite flexible, folding back against the creatures body.

Continuity

The landing crew are shown walking down the ramp and wading through water upon landing; when running back to the ship the land is dry and they walk onto the boarding ramp on dry ground, when the camera angle changes we see water around the ramp again.

Incorrectly regarded as goofs

When Daniels and Tennessee eject the trucks from the cargo bay, they start to fall towards the planet.

The Covenant spent most of the movie very close to the planet's surface, including near the end meaning the planet's gravity would have an effect on the truck. If the Covenant had been orbiting, the trucks would have merely trailed behind it in the same orbit ; but it was effectively hovering over the planet, so they fell out.

Plot holes

David claims to have created a "perfect" organism, while in fact the organism he "carefully selected" is inferior to the basic airborne viral organism that attacked the crew when they landed. New "perfect" organism requires eggs/embryo, "gestation period" prior to which a clearly visible "face-hugger" is attached to the host and etc.

Continuity

The blood on Ferris's face changes from scene to scene.

Factual errors

Synthetics (Robots) do not grow hair, as David did mid-way through the film. They do not age. They stay the same throughout their immortal life cycle.

Continuity

In the shots of the first Neomorph emerging, Ledward's uniform can be seen covering parts of his lower back and arms, but immediately after the alien exits and Ledward slumps backward, his uniform is not covering him at all.

Factual errors

Near the end of the film, David asks the computer ("Mother") to play the entrance to ValHalla from Act 2 of Wagner's "Das Rheingold". The opera consists of 4 scenes in a single act, and the music is from Scene 4.

Factual errors

Free climbing is with ropes as back up. Solo climbing is what they should be referring to.

Incorrectly regarded as goofs

When Walter and David are quoting from the poem Ozymandias it is incorrectly identified as being written by Byron. It is in fact by Shelley. However, Walter later corrects David on his mistake, revealing that he is not as perfect as he thinks he is.