Why does the Scottish guy start as a hard arse security merc who doesn't like the biologist then change to a scared of the dark Geologist who runs off all chummy with said biologist?
Why does Charlize Theron seem surprised to see Weyland on the ship when she knows David is talking to him (unless there's a better interpretation of their confrontation when David is wearing his visor thing?
Why does everyone seem to forget that Elizabeth has just knocked out two scientists, performed a cesarean, run out of a room with her stomach stapled shut & leaving an alien squid thing in the escape pod for 20 minutes after the scene?
Why does the biologist randomly turn up as Nemesis from Resident evil (other than to kill off the strenuous ship crew)?
Why, given the site seems to be isolated, are there "hundreds" of other alien ships littering the moon, apparently in a similar state of stasis?
Why does David appear to pull what looks kind of like a face hugger, or at least something alienlike, out of the canister, but otherwise they just ooze goo?
Why does David infect the archaeologist with the black stuff? If the answer is because he knew doing so would lead to Elizabeth getting pregnant with the squid baby, then why is he interested in making an alien baby?
Why does the alien head they find explode in a way not dissimilar to how the aliens body at the beginning disintegrates?
What happened to the aliens that fled into the chamber full of pots of goo?
I've ignored the things that bugged me but can be put down to standard sci-fi cliches (no guns on the science exhibition; taking their helmets off; David wanting to kill his creator; captain & flight crew blowing themselves up for greater good etc etc)