Just saw this movie so maybe it has already been brought up on this thread but it seems wrong that the engineer got out of the chair that controls the ship.
In Alien we see the engineer sitting in the chair and so in Prometheus when the engineer sits in the chair and puts the helmet on I thought, " oh so the chip crashed and the folks in Alien see him dead in the chair." But he got out of the chair and ended up dying outside of the ship...so who is in the chair in Alien? Seems like an obvious blunder that everyone creating the film should have noticed way before filming even began.