Plot hole: If the dinosaurs are so dangerous, why are they only kept behind plastic sheeting at the back of the truck, rather than in cages? There are computers in the truck, so obviously people must go in there, and it wouldn't be very safe to use computers if dinosaurs were roaming free in the trucks.
Plot hole: When the female marine is killed by the T-Rex on the ship, it busts through the bulkhead of the ship, despite the fact that ship bulkheads are made of reinforced steel to withstand the pressure of the sea. Also, a few minutes later, the scientist and marine commander are hiding in a metal crate, but the T-Rex is now unable to get to them, even though the walls of the crate would be far less structurally sound than the bulkheads.
Plot hole: The marines lure the dinosaurs into the ship, but there is no way they could lure the T-Rex into the bowels of the ship. It barely fits in as it is, and all the corridors leading down to where it is are too small for the T-Rex to fit through.
