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.

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.

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.

Factual errors

During the opening act, the Covenant is damaged by a "neutrino storm." However, neutrinos are nearly massless particles which so rarely interact with other material that they commonly pass though the entire Earth without ever causing a reaction. They could not damage the ship as portrayed in the film.

Factual errors

When Daniels and Tennessee open the terraforming bay doors at the end, the ejected trucks fall planetward as if the Covenant were hovering rather than orbiting. Earlier, however, shortly before Tennessee descends in the cargo lift (~1:16:45), a full screen monitor displays "COVENANT ORBIT", hence the ejected trucks would stay in orbit until they lost significant velocity, and not fall as depicted.

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.

Factual errors

At around 24 mins, the Covenant's computer is saying the location of a signal's origin in astronomical terms. It incorrectly says "declension"; the correct word is "declination".

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

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 Richard Wagner's "Das Rheingold". The opera consists of 4 scenes in a single act, and the music is from Scene 4.

Continuity

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

Plot holes

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.

Audio/visual unsynchronised

In the second half of the movie, in the first scene where Daniels is sitting on the ground out in the rain by the laptop asking the crew on the ship to drop the cargo lift we can hear her voice loud and clear, but her mouth is not moving.

Plot holes

In Prometheus, it is established that synthetics like David do not breathe, yet after he fights Walter but before he runs to the cargo lift rescue, he stands at the top of the ramp to look back, clearly out of breath. He also tames a creature by breathing on it and plays the flute.

Factual errors

Mother gives distances in metric kilometers, but reports the planet's air pressure in psi (pounds per square inch) instead of kPa. A program like this would not mix and match.

Plot holes

a supposedly well-trained crew take no precautions at all against infections from an alien biosphere. They had no reason to suspect a link with humans, but Earth has bacteria like Tetanus that cannot survive in a human, but often causes death while trying.They have an android, safe from infection, but go themselves.

Continuity

When Walter removes a damaged embryo from A-3371 there is a small pool of red liquid remaining in its holder which then completely disappears seconds later when he closes the drawer.

Character error

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 Lord Byron. It is in fact by Byron's friend Percy Bysshe Shelley. However, Walter later corrects David on his mistake, revealing that the "perfect" David is in fact deranged.

Plot holes

the Engineers in the city take no precautions whatsoever against a strange ship.

Miscellaneous

In this, and every other film in the Alien franchise, the creature grows from a homunculus within a human body cavity to full adult-size in a matter of hours with no explanation as to the source of the additional mass necessary for such rapid growth.

Revealing mistakes

When Ledward,first person who was infected sit on rock feeling sick we see two mosquitoes around him,and there is not supposed to be any animal life form on planet,except aliens.

Factual errors

Neanderthals are described as discovering music and then inventing culture. Neanderthals were a cousin species, 98% replaced by modern humans from Africa. Their culture was static and had no confirmed art, which begins with modern humans.