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: 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.
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?
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: When Leo, Gustav and Himmel are driving through Miami looking for Pest, Gustav notices that the tracking device that was put in Pest's underwear shorted out because of how much he was sweating. An earlier scene showed that Pest jumped off a boat in the middle of the ocean and swam to Miami. Since the tracking device was in Pest's underwear the whole time, it should have shorted out the moment he jumped into the water leaving Pest safe and Leo, Himmel and Gustav driving around aimlessly.
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: Barry gets killed violently at the pageant. So obviously there should be blood everywhere. When the police go up to the crime scene, they find nothing. There's no way the killer had time to clean up anything, let alone drag away Barry's body without someone seeing him. And blood starts dripping after the police leave the scene.
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: Kazam is supposed to be a math genius, something that the plot hinges on, but he makes several mistakes when calculating the number of prime factors to find out whether a room is trapped or not. He says that 462 has three prime factors, when it has four, that 206 has four when it only has two and that 563 has two and 911 has three when both are actually prime numbers.
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 is highly unlikely that the murderer knew Phil was going to put his ear to the stall when he heard the babbling. It is even more unlikely that the murderer is going to get him on the first stab through the stall. (Which also requires a lot of strength). We also have to assume that he spent time hanging out in the bathroom knowing Phil would go there to begin with, and that other two men with weak bladders were doing the same simultaneously forcing the victim to go to the stall to begin with. (00:07:45)
Suggested correction: The killer is incoherently whispering in a strange way in the adjacent stall to lure Phil to press his ear up against it. After stabbing him through it, the killer inspects the knife inquisitively, as if checking to see if he actually got him. While it's still not a terribly plausible scene, the killer's demeanor suggests that he encountered Phil in the restroom by coincidence and improvised the kill, rather than anticipating all of Phil's actions as part of a perfectly executed plan.
The general logistics and planning of the murder are a separate issue - because no, the murder was planned. The entry just says that it's "highly unlikely", putting it mildly, that the killer could guess the exact position Phil would pick to listen to the noise. Just a few inches up or down, left or right, make a huge difference. The killer looks at the knife admiring the results, because if he had any doubts that he got his victim, he'd be trapped in a bathroom with a screaming, wounded, angry Phil and plenty people who could come and help.
To be more clear, the correction here is that Phil had heard strange talking/whispering rather than music, which makes it at least a little more plausible the killer would think he might put his head up against the wall at a certain spot. Unlikely for sure, but unlikely isn't a mistake, it's just what movies do. Phil's death was planned yes, though it stands to reason the plan was more "surveil and strike when vulnerable" and less "wait for him in this particular stall we know he'll be next to."
Plot hole: During the Congressional hearing, it is suggested that the alien signal could have been faked from a satellite - as Ellie only has her own experience to go on, it leaves her believing what happened, but still with an element of doubt. However, as a professional astronomer, Ellie would have immediately dismissed this since a simple parallax (triangulation) would have confirmed that source was at the distance of Vega - a distance far too great for any rocket to reach. (This is mentioned in the book). In fact, this is mentioned early in the film, when the employees in New Mexico calculate the source of the signal while it is transmitting prime numbers.
Plot hole: It takes less than 3 minutes to fill the house with water using a mere garden hose? I mean come on...
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.