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.
Revealing mistake: In one shot when the boat is pulling away from the waterfall, you can clearly see that the shot is the same one they used earlier in the movie. The water from the waterfall now is going up the cliff! They have just put it in reverse.
Factual error: The Russians stopped using steam locomotives in the 1970's. So bringing one out of retirement in 1997 to haul nuclear warheads would mean that your highly secret nuclear train would be well known among rail enthusiasts for weeks before.
Deliberate mistake: Leaven spends too much time thinking about if 645 and 372 are prime numbers to be believable. But she knows the factors of 649 and the result of 26 to the power of 3 almost immediately. Plus anyone with any maths knowledge whatsoever would know that any even number (or one divisible by 5) can't be prime, so 645 and 372 could be dismissed without even thinking about it.
Plot hole: When Andy turns into a werewolf, he kills both Amy and Detective Benbou. Later in the morgue, Amy tells him because of this that she is forced to become his "rotting sidekick." If this is completely true, then Detective Benbou should also be following Andy around but he isn't seen after Andy manages to escape from the morgue.
Factual error: The plastic explosive used on the cockpit door was C-4. When shot (as shown), C-4 does not explode; it requires the use of a detonator.
Suggested correction: You can see him applying a detonator prior to him shooting it.
If he applied a blasting cap (detonator) he should have used it then. Just putting a detonator into C-4 doesn't all the sudden make it vulnerable to being shot, he would have to actually hit the blasting cap's wire, which is about 5mm thick and relatively short (and it would have to be one that's sensitive to gunfire). Not a very probable shot, even less so when he doesn't even look when he shoots.
Plot hole: In the scene where Ashley Judd runs away from her attacker and falls into her aquarium he has moved to the bottom of the stairs - there is no way he would have been able to move that full fish tank. It looked to be about a 30 gallon tank - it would weigh about 400 pounds with the stand and even if he slid it with some superhuman strength, glass tanks are notorious for shattering when you move them full. Plus it would've made enough noise to wake the dead - no way she wouldn't have heard it.
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?
Continuity mistake: The whole big prison bus escape scene revolves around Chris Tucker being handcuffed to the French guy, but when Frenchy's friend arrives in the bus he stands up and hugs him while the handcuff is shown completely unlocked from Tucker's hand. In the next shot and the entire next scene they are still handcuffed together.
Continuity mistake: In the beginning of the movie, when the little girl is falling, they film her falling all the way down backwards. When they flash to the young Simon's face and the priest and back to the girl she lands face down.
Visible crew/equipment: In the shoot 'em up scene at the hangar near the beginning of the film, right after Tito and Wanda take down Pollux, when Troy shoots an agent in the stomach and the agent flies back - you can see at least two cable wires pulling him backwards. You can first notice the 2 wires when the agent is running in slow motion right before he shoots him. (00:14:15)
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.
Factual error: Just before Declan and the Jackal start shooting at each other in the subway tunnel, one of the trains starts coming from the opposite direction and begins passing Declan. This train continues to pass him at full speed for a full 35-40 seconds while they shoot it out. Subway trains are not nearly long enough for that. Also, during this time another train comes from behind him and he has to get between them and hold onto the light for a few seconds while they pass. But the second train then passes first while the first one passes fully about 2 seconds after the second one came... and it got there first, by about 15-20 seconds. Subway lines are about the same length as each other as well. But the first one was way longer and way wrong. (01:49:30 - 01:50:05)
Revealing mistake: When the killer is attacking Cici on the balcony, you can see blood on Cici's back before she is even stabbed and both times she is stabbed, the knife that comes out of her back has no blood on it. (00:33:20)
Character mistake: When they're on the island and the INGen helicopters are flying in, Jeff Goldblum takes the binoculars and looks through the wrong end. (00:32:30)
Revealing mistake: When Batman places the heaters around the telescope to thaw the ice, the frozen floor moves like plastic when he places the second heater. (01:45:00)
Continuity mistake: Toward the end, Carmen Ibanez gets stabbed through the shoulder when she is brought before the big master alien thing. If you were to sustain such an injury, there would be so much swelling, not to mention just destroyed tissue, that you wouldn't be able to move that arm for weeks. Yet a few minutes later, she is seen hefting around a very large assault rifle, and seems to have no difficulty. I guess it's a pretty standard action movie "heroes can temporarily ignore injury in order to save the day" kind of oversight, but it just seems exaggerated in this case, considering how severe the shoulder trauma looked. (01:48:15 - 01:53:40)
Continuity mistake: After Barry has jumped into the water reclaim the crown, he comes out of the water with a perfectly clean shirt, but in the next shot the blood is back on his shirt as expected. (00:22:50)
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)
Factual error: The geography around the VLA in New Mexico is actually relatively flat - in fact one of the reasons why the array complex is there is because the land is flat. The canyon in the film was actually Canyon de Chelly, in Arizona, more than 170 miles (270 km) away. But in the film, when Ellie goes to the canyon, the radio antennas seem to be right there, insinuating that the canyon is part of the VLA's magical desert scenery.