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: When Morgan and her Slave/New Boyfriend are escaping from the burning ship, which is going to explode any second, they emerge onto the deck, run up a flight of stairs, cross the deck to the stern rail, look about themselves, then dive overboard. They know the ship is about to explode and are desperate to get overboard. The railings are about a metre away from the hatch they emerge from in the first place - why not just jump overboard there?
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: Now why the heck is one of the stealth fighters anywhere near the train? Stealth fighters use advanced targeting and do not need to be anywhere near their target, yet in the movie the one fighter is so close to the train when it gets blown up that it looks like it's on a collision course.
Plot hole: When they are on the subway train, they are talking about the worm and the virus. They said that everything would happen on the 14th. A couple of scenes later, when they are setting up for the traffic lights to go crazy at 9:00, Dade looks at his watch. You can see the date as 10-18, which is 4 days afterwards. (01:17:15 - 01:22:50)
Plot hole: The group poison a dozen or so people and dispose of their bodies by burying them in their own garden. Some of their victims are notable celebrities - television presenters, authors, leaders of large and vocal pressure groups. Certainly some of them are nobodies, but nonetheless they are going to tell friends where they are going for dinner! Not one of these people told their assistants or their secretaries or a friend or a relative - a spouse? - where they were going and what they were doing on the night they were murdered? Not one of them? Not one single trace was left for the police to follow? Absolutely impossible.
Plot hole: When Jack first gets the diskette after arranging the theft of Angela's bag, he cuts his hand to show he struggled with the thief. The next scene shows them on his boat, a few hundred yards from shore, where Angela is helping dress the wound. They then speak of calling the police. When they'd just walked along the beach from the resort, and with the hotel in the background on shore in the scene, why would they take the time & trouble to (presumably go to a dock), get on the boat, drive out a few hundred yards, stop the boat, sit down and THEN deal with the wound, and talk of the police, instead of simply walking back to the hotel & getting it all dealt with immediately? (00:29:00)
Plot hole: For the transaction with the buyers, Moore sets up two hotel rooms: one where she will be based and the other for the buyers. She also goes about setting it up so that her toy truck can be navigated through the ventilation system, with a camera and having a private speaker system between them. Now when Banderas finds the room with the buyers he is unaware of where she is but knows she's close and checks the hotel's billing system on the television. On the TV the room number she registered with is shown. She went to all this effort to protect herself and yet registered the other room in her name and linked it with her room? Its not like she would have missed something so important because she would have needed to sign in when checking into the hotel. It seems to only serve the plot as Banderas relied on this information to find her and make his move to try and eliminate her.
Plot hole: In the scene where William takes Murron for their initial ride, he shows up in pouring rain, yet all further shots show the two of them totally dry. The tone of her mother's voice when they get back suggests they did not spend the night together, and the whole sequence appeared in a couple hours. They could not have gone from soaking-wet to bone-dry that fast.