1.Why would a trillion dollar space mission not have all of the crew get to know each other before they leave for an alien world (and possibly never come back)? I guess if the orbit of the Earth was such that they had to leave ASAP in order to not waste fuel, it kind of makes sense, but with a state of the art spaceship, what's a couple light years?
2. David can watch the dreams of the sleeping crew (and even communicate with a sleeping Weylan), but nothing really comes of it. The video of the girl playing violin (presumably Shaw) kept popping up: David tries to send the video of the girl in a message (to Earth?) and gets no response. After the crew is awakened he tries again, with Shaw and Holloway present, so it wasn't a sneaky move on David's part. At the end, when Shaw enters the damaged lifeboat, the same video is playing on the giant screen in the main room.
3. How the hell did Fifeld and Millburn get lost anyways? Couldn't they have asked the ship to triangulate their position with the pups so at least they were close to the exit when the storm passed? Wouldn't any place be better than the weird room where a bunch of Engineers died?
4. Janek has a pretty laid back attitude considering two of his crew is lost in a giant dome where something violent happened. Any space mission would have something similar to a black box, so even though Janek was conveniently banging Vickers, he should have been interested on what happened while the bridge was empty. Also, why was the bridge empty?
5. Nobody cares that Shaw was impregnated with an alien and removed it herself. She manages to get into the lifeboat and use the state of the art surgical robot with nobody noticing, and when she stumbles upon Weylan, nobody questions her appearance or the fact that she's in her underwear and covered in blood. And what was with her diaper-style panties and bra? Did she forget to pack her own undies?
6. Janek, Ravel and Chance decided to sacrifice everyone in order to destroy the Engineer's ship, as if none of the other crew matter. Speaking of the rest of the crew, with all those extras there's way more than 18 people on the ship (including Weylan).
7. There are earthworms in the alien temple, probably for no other reason than Ridley Scott thought that looked cool.
8. At no point in the movie do any of the characters express surprise that a) they discovered alien life and b) there is a real android in the crew. The former is simply bizarre, but the latter has precedent in Alien. When the crew discovers Ash is an android, they say that it's not normal WY protocol to put an android on the ship.
9. When Ash and Bishop's heads were removed, they died soon after. When David's head is removed, he can not only survive but pilot a ship.
10. There was literally no reason for the Vicker's character to exist in the movie. The only thing of consequence she did was kill Holloway with the flamethrower, which could have been done by any of the other anonymous crew members.
11. There were at least 3 other domes behind the one they entered, each with a C-ship under it. How do David and Shaw know the one they took at the end doesn't also have a giant cargo load of alien goo? How is Shaw going to survive on the ship with a cryo tube made for a creature 3x bigger than her, with no food or water?