When Gully puts Dr. Clapton in the back of his station wagon, he is not wrapped up or tied up. When Gully arrives at the minesweeper where he is to hold Clapton captive, he takes him out of his car, and Clapton is now inside some kind of large canvas bag.
On the Colonel's uniform, the Eagle insignia and the Army Infantry crossed rifles on his shirt collar are worn incorrectly. Both insignia should be right side up, not sideways.
During the shootout with police and MPs at the Army Paymaster's office, a woman in a blue dress can be seen calmly strolling behind the line of police as they lay down a tremendous volley of fire. She's about 50 feet behind them, in harm's way, and makes no movement of any kind to indicate she's aware of the mayhem around her.
The first shot of McGarrett when he is walking down the corridor in the hospital is printed backwards, as his his hair is combed the other way.
It would be rather far fetched to think that Dr. Clapton's body would easily fit into that small compartment in the back of that station wagon. It would have just enough room for a tire iron, and jack.