The movie suffer from various cuts.
The trailer is full of scene missing from the movie or with some differences.
For exemple :
The Engineer do not strangle Shaw against Vickers quarter Chandelier, there is no fight between them has it seem to be.
The engineer arrives, push Shaw near the medpod door, Shaw opens the door and voila!
Remember that shot of the Mercs shooting in the hangar and behind them Peter Weyland getting out from the sas with his suit on helped by David? In the movie the mercs shoot but the door is closed. Wayland is still not suited he's in his room talking to Shaw.
Thats shot of Shaw driving inside the big truck, acting like she's doing rear driving?
Never in the movie you see her doing that.
Definitly there is an extended cut to come.