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: 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: 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: After Sid and her friend get out of the car, they run away from it. Yet somehow while they are talking, the killer climbs out of the car and ends up behind them without them seeing a thing.
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: 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: An engineer on a rescue ship seems to be the first person instead of the entire planetary intelligence community and the NSA (as reported by Dr. Wier) to translate basic Latin from what the Event Horizon's captain said. Somehow nobody else with all the vast resources of the NSA and other government organizations could clean up the transmission to determine exactly what was said?
Suggested correction: The recording of the Event Horizon's captain was taken directly from the ship's log. It was only available to the crew of the rescue ship at that time.
No, the NSA and the military had that transmission themselves as it's Dr. Weir who plays it for the crew before they reach the Event Horizon. How would Weir have it if they didn't obtain the log until they got to the ship? The part that they had, and DJ heard incorrectly, was received by the government agency in charge, leading them to send the Clark into Neptune orbit for a search and rescue of the crew and the ship.
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.