Plot hole: The convicts remove the radar transponder from the Conair aircraft and put it aboard a tour plane to distract their pursuers. That won't work. By law the tour plane will have a working radar transponder of its own, and two working transponders that close together will show up on radar as a collision. Air traffic controllers would immediately alert emergency services who would, obviously, wonder how two aircraft that had collided had managed to stay in the air. Nobody disconnects the first transponder - Pinball carelessly tosses the second transponder under the rear seat of the aircraft (the implication being that it continues to operate, perhaps on backup battery power). He doesn't disconnect the original transponder either - Swamp Thing, a skilled pilot, does that. There is no time for him to do any of this before he is stopped by the female security guard anyway.
Plot hole: In the final showdown, when Bond is fighting with Stamper, the girl is wrapped in a chain, hanging from a crane and dropped into the sea. After the boat blows to bits, the chain continues to hang down, even though there's nothing holding it. It even keeps hanging after Bond's swum down to untie her. What's keeping it there? Do all stealth battleships come with buoyant chains? With both arms at least partially free, why doesn't she just climb back up the chain?
Plot hole: Dafoe and Bullock leave the ship a long time before it hits the tanker and there is a lot more time before it crashes into the town and even more before Alex gets on that speedboat. No matter how fast he could have gone, there is no way he would have caught up with them.
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: 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: When the diesel train stops in the tunnel, one of the soldiers tells another one how far they are from the spot where the nuclear detonation will take place. Do the math: the distances don't work out. At least one of the trains would have to do over 100mph AVERAGE to put enough distance between them. Military precision, indeed.
Plot hole: Wouldn't the bomb (when in the back of the truck of the bad guy driving away) vaporize him, considering he wasn't that much far apart than Allison was when she was tied up? He is even quoting as "Are you comfortable? Well it doesn't matter considering you'll be vaporized before you know it," when she was about 4 ft away.
Plot hole: The main criminal puts on the "butt inspection gloves" whilst searching the first house, but when Alex sees him through the telescope he pulls down the blinds and has black gloves on. Returning outside, they revert back. However, how does Alex know the criminal donned the rubber gloves (when he describes him to his mother), if he saw what we saw through the telescope - the black gloves?
Plot hole: It takes less than 3 minutes to fill the house with water using a mere garden hose? I mean come on...
Plot hole: The policeman survives a frontal crash into the hillbilly's truck at full speed without as much a scratch. (00:24:40)
Plot hole: Part of the reason that the Jackal killed Lemont, asides from him being very annoying and money grubbing, was the fact that he wasn't going to give up the blueprints and plans for the device he made for him. Made a big deal about how he had to turn it over, and he tricked Lemont into going out into the testing ground with him so he could kill him. Then in the next couple scenes, the FBI is investigating Lemont's warehouse after they find Lemont's body, and Delcan finds the plans for the device Lemont bluilt for Jackal. This makes no sense. The Jackal was so adamant about getting those plans back, and even killed Lemont over it, it's just baffling to think that he would not have returned to the warehouse to get them after disposing of Lemont. Not doing so lets the FBI find it exactly as shown in the film. The Jackal is show to be very intelligent and has been doing this line of work for 20 years. And as Declan says, he's not inclined to make mistakes... Especially a mistake like that. (01:02:35)
Plot hole: When they are trying to find a way to stop the lava from going in to the museum, Tommy Lee Jones has an idea to push a bus up against the museum to divert the lava. The plan works but the lava does not melt the bus like it melted Tommy Lee Jones' car or the fire truck. Even though the bus melts later in the movie, it doesn't melt it instantly like it did with the fire truck.
Plot hole: When Chris Tucker phones his girlfriend from from the mansion, we see the 2 detectives, staked out in front of the girlfriend's house listening in on the call and trace the call to Beverly Hills. At the end of the call Tucker tells her that he's "on his way over". The detectives apparently aren't too concerned about this or forget, as when Tucker shows up, they are still casually sitting in the van. They haven't called for backup to set up an ambush or anything, no, -one of them is asleep and the other decides they should go check out the girlfriend's apartment after seeing a light go on.
Suggested correction: As we who have seen the film all know, ol boy with the grey/white hair is actually a crooked cop and the younger hothead listens to him. Even when Tucker shows up at the house he still doesn't reveal that he is a crooked cop, not until he has the diamonds does he do that. It makes perfect sense for them not to call for backup, and they use her turning the light back on as proof that he has shown up showing that they heard him say he was coming.
Plot hole: When Quinn is in the airplane, trying to get away, they are already above land, with civilization (you can see some buildings). There goes the whole isolated theory.
Plot hole: When Ann and Runaway are fleeing from the dinosaurs in the car, suddenly a fence flaps into the screen and blocks the ways of the running dinosaur. This makes no sense and is never explained, since none of Ann's friends or anybody else is anywhere around there to manage this, nor is the fence ever mentioned, nor is there any other (reasonable) reason that the fence would block the way exactly in this moment.
Plot hole: A Bug meteor knocks out the Roger Young's communications. She dodged it at sublight maneuvering speeds, indicating that it is moving fairly slowly. If it is so important that she warn Earth it's coming (which is how we know their comm was damaged), why doesn't she jump back to tell them or destroy it herself? Even if she has no capital ship weapons (she is a troop carrier), there is no indication that her faster jump drive is damaged or needs longer than they have to warn Earth to charge for a jump, or that she can't leave her patrol station, etc.
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.