After Murdock and Hannibal swim out to the chopper an take flight to chase down the boat launch, Murdock still appears wet in the cockpit, but Hannibal is completely dry.
When Murdock got into the rescue helicopter he had long pants on, but in another view the pilot had shorts.
When BA and the team are heading toward the plane for their planned escape, the section of the plane that was prepared for the vehicle to crash through is visible.
During the aerial view of the ship, as the distress call was going out, the fluttering of the filming helicopter's main rotor blades can be seen at the top of the screen.