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.
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.
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.
The blood on Faris's face changes from scene to scene.
When the energy sails are nearly deployed, we see a computer hologram depicting their progress. This hologram has the sails moving much faster than the actual sails shown in exterior shots of the ship.
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".
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, 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.
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.
When the crews are on the planet, at various points, the beams from their laser sights are sometimes obviously misaligned with the weapon's barrels, notably canted up on occasion.
When the small ship detaches from the mother ship in orbit, the ship accelerates toward the planet. In order to achieve atmospheric entry from orbit, deceleration is used to allow the planet gravity to drag you in at a much lower risk of burning up. Even with the possibility of future materials that could possibly withstand the heat, this practice would still be used to preserve fuel.
During the opening act, the Covenant is damaged by a shockwave after Mother detects a "neutrino storm". 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. However, the ship wasn't damaged by a neutrino storm at all, but by (as the crew puts it) a "highly charged shockwave from a stellar ignition" (e.g. a supernova) and/or a "spontaneous stellar flare". A neutrino burst is merely something that occurs during a stellar ignition event but is not the cause of the event or any resulting shockwaves from it.
After David cuts his hair after meeting Walter, the color of his hair changes from blond to brown. David would not have a way to color his hair, or even that quickly, on a primitive planet. However, we can see that David's hair has darker roots (he was seen bleaching it in Prometeo (2012) to look like Peter O'Toole) and he was simply cutting away the remnants of blond that he had allowed to grow in the intervening years.
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 creature's body.
The neomorphs that are shot and injured run off through the undergrowth trailing their acidic blood, leaving no visible damage to surrounding vegetation. However, the neomorphs are a possible earlier iteration of David's "perfect" creature, and thus may have less acidic blood.
At the end of Prometheus, Dr. Shaw left in the engineers' ship with David's head in a bag. David's body was on board the humans' ship when it was destroyed. Yet, David has a body when he appears in this movie.
David was decapitated while on board the engineers' ship, not the humans' ship. The short prologue film "The Crossing" chronicles how Dr. Shaw repaired David by re-attaching his head to his body.
David was decapitated while on board the engineers' ship, not the humans' ship. The short prologue film "The Crossing" chronicles how Dr. Shaw repaired David by re-attaching his head to his body.
When the scouting troop is walking up the mountain and commenting on the strange lack of animal sounds, a rhythmically flashing white light can be seen on a distant lake that has no relation to the plot.
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.
When David abruptly stops playing the piano to ask a question, the last four notes he plays are three identical notes, followed by one higher note. But to play that higher note, his hand moves left, toward the low end of the keyboard.