Plot hole: When Quinn is in the airplane, trying to get away, they are already above land, with civilization (you can see some buildings). There goes the whole isolated theory.
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: 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.
Plot hole: The use of massive explosives to separate a ship makes no sense as the explosion would send fragments at high velocity in every direction guaranteeing it would penetrate whatever ship is remaining. As we see in the final scene when the ship does blow apart, it is not a precise controlled detonation to sever connections but a total (and glamorous) explosion which makes no sense whatsoever.
Suggested correction: The explosions breach the outer hull, pulling the debris outward with the explosive decompression, the film shows the ring shaped explosions at both ends of the corridor. The debris wouldn't hit the lifeboat because it is heading in a different direction.
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.
Plot hole: They show the two men trapped inside a ring of fires that they have built, (and must constantly maintain to keep the bear at bay), as the sun is setting. And, somehow, when the sun rises, they have created enough rope, (just from grass and bark, I guess), to tie a huge boulder from way up in a tree - all wrapped with ropes and spikes, and have somehow deployed that, and stationed a bunch of other sharpened spears in various places, over hundreds of yards.
Plot hole: It makes no sense that Martin would be getting the invitation to the reunion mailed to his office (or to anywhere else.) He's had zero contact with the alumni committee, and they're not going to hire a private detective to find him. He also doesn't have contact with anyone else from his hometown who might have forwarded it; his father's dead, and his mother's not in her right mind. There's no explanation for why it would have ended up there except for needing to set the plot in motion.
Plot hole: Regis could have saved himself a lot of time and solved the case much quicker if he had just verified the entries in Carla Town's day planner with the businesses listed. A few phone calls would have told him the entries were forgeries without going to the technician for help.
Plot hole: When Luther places the envelope on the table during the White House tour, he is not wearing gloves, thereby leaving his fingerprints behind.
Plot hole: Kahn's death makes no sense. In the film, Rayden explains that the dragon tattoos flee one's body upon the person dying. And yet, Kahn is still alive and not even close to death when his tattoo flees. (Which is what kills him, since it rips him open when it flees.) It's like they couldn't figure out how to kill him in the script, so he's just spontaneously is killed by his tattoo, even though it violates the rules the film set up.