Plot hole: When Alex and Clear are sitting and having coffee they are on a corner. He looks in the window to see the bus pass, and as he looks to see if it is there, it's not. As the camera pans across the street, there is some construction going on which is blocking that whole road from being used, but then Terry, Carter's girlfriend gets "waxed" by the bus - no way it could have got through all that construction.
Plot hole: At the start when the guys are infiltrating that building they parachute down to the roof. They are dressed in black so they can't be seen, but their parachutes are white. (00:02:50)
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: When the first security guard, who stayed back to get something to eat, hears something in the laundry room, he walks over to the washing machine where he finds the head of the other security guard inside. He turns around screaming and trips over the security guard's body on the ground with no head. Wouldn't he notice the dead body on the ground when he first entered the room?
Plot hole: The movie is based on one huge plot hole: if it wasn't for the "professional" hitman's sloppy work, Bullitt and his team wouldn't have been needed for much. The hitman enters the hotel room, wounds the policeman, then shoots the target with one shotgun blast to his upper left shoulder area. Any hitman worth his fee knows that this is not likely to be an immediately fatal wound. The hitman had a pump shotgun and should have finished the job right then and there. Surely he had more than two shells. Instead, he sees the target is slumped unconscious, then leaves the hotel room without checking to see that his victim really is dead. Nothing seems to be immediately threatening the hit team, though. The hitman spends the rest of his life trying to finish his job and pays the ultimate price for being lazy.
Plot hole: In the unedited video footage of the helicopter incident shown to the crowd, the last shot of Arnie getting knocked out is seen from his perspective and as such could never have been filmed by any camera.
Plot hole: If Jack can speed the train up at the end, why does he not try to slow it down? Even if it can't be stopped completely, using the speed lever to reduce it to the minimum possible would be a sensible course of action. There is nothing to suggest he wouldn't be able to do this as he is able to increase the speed without any trouble. If there was something to show that slowing down the train would be unworkable it would make sense, but seems to more serve as a plot device.
Plot hole: Throughout the entire movie, barns, houses, cars, 18-wheelers, etc. are demolished and lifted into the air like they were made of paper. And yet Jo and Bill pass through one tornado after another with nothing more than their hair getting messed up a little. You'd think the debris alone flying into their faces at 100 miles an hour would be enough to give them a few injuries.
Plot hole: The opaque red lined map that Otomo retrieves from his first fight is ridiculous. Why would people who know where the hidden base is be carrying around a map on them (which shows a route so basic that they'd have to be brain-dead not to be able to remember it anyway) just so that conveniently one of their enemies can get it?
Plot hole: Why was $100,000,000 worth of heroin sitting in the police vault all this time before the bad guys stole it? Wouldn't the DEA have taken possession of the drugs long before that?
Plot hole: When Charlie sets out to hijack the money train, he jumps off the platform onto the tracks as it arrives, in plain sight of the driver and other passengers at the station, and only puts his mask on once he's in position on the tracks. The train conveniently stops right over top of Charlie, allowing him to enter through the conveniently-placed grate on the train's floor. (01:17:15)
Plot hole: In the end of the film it is heard the police want to exhume the body of Charles Lee Ray from his grave site in New Jersey. Now when Chucky and the crew get to the grave site they find and kill a coroner who is digging up the body. He is the only one there at 1am, by himself, a lonely coroner without any police officers, after all this is a police investigation and I doubt the cops would have him there alone. Then right at the end the Detective who is hunting them arrives. Now he is a cop from Lockport, about six states away. A. Why did he drive all that way to see the body? B. A cop from all the way down there shows up but no new Jersey cops are at the scene?
Plot hole: How did the men on the ship get killed? The bridge was intact and the T-Rex was still inside the cargo hold. [A raptor was meant to escape from the boat when it pulled in to the harbour, but they cut the scene from the film and now that bit doesn't appear to make any sense.] (01:40:55)
Plot hole: When Nick confronts the P.I. and yells "Why are you following me?", he looks inside the car and see the file with his picture on the front seat. The P.I. notices this and turns the file over. After Nick grabs his gun, the P.I. jumps out on the other side, raises his hands in the air and tells him someone hired him and runs off. As the P.I. runs off, Nick yells "Who hired you?" as he stands alone next to the car. He then waits a minute and walks off. If he really wanted to know more information, he could have taken the file that was right in front of him on the carseat. It makes no sense that he is desperate for information about the strange events that are going on, sees this file on him, and yet doesn't even pick it up or look at it. (00:59:55)
Plot hole: After an assault on the scale that's been witnessed, covering a wide area of London by extremely well prepared attackers, there's no way Marine 1 would fly to the airport at low altitude within easy range of missiles, and then when attacked, double back over the areas that have already been attacked where hostiles would still be present. (00:35:00)
Plot hole: The admiral receives the news of the stolen aircraft from the general over an open radio, with umpteen enlisted personnel within earshot. However, when the air group commander asks what the OP is about, the admiral tells him that it is on a need-to-know basis.
Plot hole: How could the police miss finding Cybil in the trunk of Michael Zane's car when it was in an impound lot? They would have definitely searched the car if he was found in violation of a federal offence (for carrying the weapons). Even if they didn't do a search, they would certainly have heard the sounds that Cybil would have made from being locked in the trunk.
Plot hole: The nuclear codes are stolen and the Russian guy holding them was let go by Dom. He would contact his government to let them know and the codes changed. Cypher would also know this so her plan is flawed.
Suggested correction: The idea of raptors being on the boat is a myth (likely spawned from a similar thing happening in the first book's ending). Though it's very poorly communicated and leaves many unanswered questions (the captain's hand the least of which), the dead hand holding the cargo hold controls implies that the T-Rex somehow got free, killed the crew, then was either lured or willingly returned to the hold where a dying worker closed the doors again.