Velociraptors on the boat were not seen in the film, neither was anything about it mentioned by any character, therefore it did not happen. Its a mistake, pure and simple. It's implied that the crew were all killed by the T-Rex as it must have broken free from the hold. The dead guys hand holding the button suggests this. the T-Rex must have went back into the hold at some point and a mortally wounded crew member pressed the button to shut it again. That im fine with. It makes sense. Everybody went up on deck to try and get the T-Rex back into the hold and they all got their asses handed to them.
The arm in the bridge is a simpel visual f**k up that cant be explained. They put it there because it looked good and it was shocking. They didnt think that at the time that it made no sense at all. Its a flub, plain and simple and cant be explained rationally other than guessing and making up shit that we dont know. The film itself implies the T-Rex did it and nothing else.