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: 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: 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: 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: 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: When Ann and Runaway are fleeing from the dinosaurs in the car, suddenly a fence flaps into the screen and blocks the ways of the running dinosaur. This makes no sense and is never explained, since none of Ann's friends or anybody else is anywhere around there to manage this, nor is the fence ever mentioned, nor is there any other (reasonable) reason that the fence would block the way exactly in this moment.
Plot hole: A Bug meteor knocks out the Roger Young's communications. She dodged it at sublight maneuvering speeds, indicating that it is moving fairly slowly. If it is so important that she warn Earth it's coming (which is how we know their comm was damaged), why doesn't she jump back to tell them or destroy it herself? Even if she has no capital ship weapons (she is a troop carrier), there is no indication that her faster jump drive is damaged or needs longer than they have to warn Earth to charge for a jump, or that she can't leave her patrol station, etc.
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.