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: 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: 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: 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: 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: In the scene where Lewis and Clark nearly hit the Event Horizon, One of the crew is calling out the closing distance and another confirms this information. Regardless of clouds obscuring their view they were aware of their proximity and the fact that they were speeding towards it and forced to attempt an abrupt stop makes no sense.
Plot hole: Susan theorises that the insects have evolved to resemble people because of predatory pressure. However, for this to be true people must have been killing them - apart from the handful of 'moles and junkies' (who were the prey, not the killers) this film shows the first contact between humans and the evolved 'Judas bug'.
Plot hole: What happened to the two boys who stayed in the museum past closing, after the homeless guy seemed to attack (or at least be seen to be stalking) them? The next time we see them, it's the next morning, and they're fine. So where did they go? Who helped them? What happened to the homeless guy? The boys couldn't have just hidden, as the homeless guy has been in the museum for ages, and these two boys just got there that day. The homeless guy would have known all the nooks and crannies and every little hiding spot available; he would have caught them.
Plot hole: Interesting to note...in the opening scene where Pete is talking to Jack, Pete says that the boiler pressure needs to be dumped every night or it'll blow because the safety valve has been rusted shut for the last twenty years. Then he continues on to say that last year's caretaker, Grady, killed himself, and he was alone at the hotel. So...why didn't the boiler explode last winter? (00:02:20 - 00:05:55)
Plot hole: Al Simmons' reasoning for wanting to quit A-6 is because he learns his rocket attack in his assassination mission in the beginning of the film yielded civilian casualties. This makes no sense, as he blatantly gunned down several innocent men in the air control tower just moments before.
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.