Plot hole: Anderton's wife gains entry into the jailhouse using her husband's eyeball - but he's already locked up inside, so his eye would not still have access to enter as it pleased. Any place anywhere that would have any sort of security system requiring anything from a simple passcode to a card key to a retinal scan, would immediately delete the user in such instances from all rights. And would also certainly report on any attempted use of such (retinal scan, pass code, whatever). (02:00:45)
Plot hole: In Paris, why does the assassin go to the ridiculous amount of trouble of swinging into the room on a rope with a machine gun when he came in from the lobby (as proved by the dead woman downstairs)? Alternatively, if his intention was always to surprise Bourne by coming in through the window, why venture downstairs at all? (00:44:07)
Plot hole: At the beginning of the movie, Hedwig rattles her cage, and Harry says apologetically, "I can't let you out, Hedwig; I'm not allowed to use magic outside of school." But he wouldn't have to use magic to let her out - the key is visible sticking out of the lock on the cage, so all he would have to do is turn the key. (00:01:10)
Plot hole: The psycho coed murders her lecherous professor (played by William Shatner) by pushing him out a window. In the very next scene, she's driving around with his body propped up in the passenger seat of her car. She weighed no more than 100 lbs., tops, and Shatner was easily at least 250 when this film was made. No way she could have dragged him to her car and lifted his dead weight into the seat, no matter how much adrenalin she was pumped with. Physically impossible.
Plot hole: Holmes asks what had frightened Sir Charles enough to make him run away from the house. But when Dr. Mortimer described the scene, he only mentioned that at one point the prints did not show heel imprints. It is an easy deduction that sir Charles had been running, but the doctor did not say anything about the direction of the footprints.
Plot hole: Clint Eastwood's whole investigation/solution is based on him suspecting that the victims had a common tie, rather than being random. The problem is there is no reason for him to think this - there is no reason given for them to not be considered random victims. For him to think otherwise was a bit far fetched. In the book, however, they were all on the organ donor list, which led him to the fact they all had the same rare blood type and so on.