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: In the air vent, we see a rat. Wouldn't rats in the vents set off the alarms on a regular basis, because the lasers were on the upper side of the vent?
Plot hole: When Butthead pushes Beavis out of Muddy's car, Beavis causes a huge car crash. Then, a few seconds later Butthead falls out and causes cars behind him to crash, but the crash that Beavis started made a barrier along the highway, so how could those cars get behind Butthead so fast? (00:51:50)
Plot hole: Slater decides to render the nuke inert by punching in the wrong code three times. However, when he does this, the nuke becomes armed, and Travolta reveals that he is one step ahead by having used a special kind of circuit board to produce this result. Two questions: One, once Slater has armed one nuke, why not arm them all? You've got nothing to lose, and you can keep Travolta from getting them for whatever evil purpose he has in mind. Slater plans to send them all to the bottom of the copper mine anyway, so just arm them all. Two, Travolta later arms a nuke himself, and then smashes the keypad with his gun. Well, if you can do that, why doesn't Slater just smash all the keypads as soon as he gets the nukes? Travolta would be defeated; movie over.
Plot hole: How would Arnold know about the cop hitting the bus when he was running away from him during the parade? He was far past him at that point.
Plot hole: When Cage is hiding the VX gas balls at the end by putting them in a drain you can see he is holding the loose ball, but then in an instant cut picks it up along with the chip.
Plot hole: The main accident is a crash involving toxic waste, which seals the tunnel, yet no one has any trouble breathing, or even has so much as irritated eyes.
Plot hole: The entire movie is a major plot hole. It's revealed early that Naji Hassan himself organized Jaffa's capture and so it follows that Hassan has no interest in the latter's release. With the nerve gas already smuggled on board the plane and the willingly suicidal Demou in place, the hijack was totally unnecessary. Demou could have set off the bomb as the plane came into land. Rather than draw attention by the hijack, Hassan could've stayed behind and made propaganda from a safe place minutes before.
Plot hole: Malloy and the others tell Snake that the Plutoxin 7 virus would cause nervous system shutdown without the antivirus. When he got back, it was revealed that it was just a hard hitting case of the flu. Why then did, at the base, the computer showing his countdown timer over the course of the film say when nervous system shutdown, not the full extent of the flu, would occur. Maybe for sake of the audience to avoid a spoiler, but those who had already seen the movie would notice this.
Suggested correction: Because the countdown timer was lying to him as well. It was programmed to do so.
Plot hole: In the beginning after Flint buries the treasure, he kills all the men that are with him. The pistols he has are one-shot pistols, so there's no way he could kill 14 men using only two one-shot pistols.
Plot hole: Why is that shark machine even there? The only reason it's there is to help the plot, and I don't see how it is of use to anyone in the corporate world. If the shark just ejects the fish it turns into fish heads out to sea, there is too much chance they will be ruined by carnivorous fish or weather before they are picked up. And fishing companies should know better.
Plot hole: When Picard, Hawk and Worf are out on the particle transmitter, they each have one gun. However, when Picard is attacked by Hawk, the gun that Hawk used is being stepped on by him. Picard left his gun over at the other mag lock, and Worf threw his away, but when the captain was in trouble, Worf had a gun. He would not have had time to run around to Picard's side before he was attacked by Hawk, so where did Worf get the other gun from?
Suggested correction: As you can see in a wide shot after Worf's suit is cut, his gun is still hanging close by. So after he closed the gap in his suit he just grabbed his own gun. Of course, he did throw it away and it should have kept on moving all the way out of reach but something stopped it. But you do see it still in reach of Worf.