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: 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: The policeman survives a frontal crash into the hillbilly's truck at full speed without as much a scratch. (00:24:40)
Plot hole: Part of the reason that the Jackal killed Lemont, asides from him being very annoying and money grubbing, was the fact that he wasn't going to give up the blueprints and plans for the device he made for him. Made a big deal about how he had to turn it over, and he tricked Lemont into going out into the testing ground with him so he could kill him. Then in the next couple scenes, the FBI is investigating Lemont's warehouse after they find Lemont's body, and Delcan finds the plans for the device Lemont bluilt for Jackal. This makes no sense. The Jackal was so adamant about getting those plans back, and even killed Lemont over it, it's just baffling to think that he would not have returned to the warehouse to get them after disposing of Lemont. Not doing so lets the FBI find it exactly as shown in the film. The Jackal is show to be very intelligent and has been doing this line of work for 20 years. And as Declan says, he's not inclined to make mistakes... Especially a mistake like that. (01:02:35)
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: 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: 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.
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.