Plot hole: How do they maintain communication between the ship at the centre of the earth and the surface? There's no wire, and radio waves can only travel any distance without obstacles, and the earth's crust would be a pretty hefty obstacle...
Plot hole: When they are being told they have failed the evaluation, the dean tells them, "Yes, you people did finish with 84%, but another one of your pledges finished with a zero in every category." It then goes on to state that this drops them down to 58%. For one pledge to bring them down 26% there would have to have been less than four pledges, including Blue, i.e. only three actually taking the evaluation.
Plot hole: In the scene where she goes to her house after escaping there is no police tape on the front door even though it is a crime scene. Earlier the police searched and taped her office - it only makes sense that they would do the same to her house.
Plot hole: The Toymaker throws that toy bird at the hippie version of himself. The toy goes through him because he is a hologram. Later, he pushes the soldier version of himself at the screen making it crack. How could he if the three others are holograms?
Plot hole: When the Drakes (Bobby's family) arrive home they are acting quite naturally, until they find Wolverine there and get a start. Later on we see that they had parked their van in the driveway right behind Cyclops' car, which Logan and company had borrowed and parked there. Wouldn't they, seeing a strange car in their driveway, be suspicious or at least enter their house asking "Bobby, are you home?" (00:52:45 - 00:59:15)
Plot hole: The fearless trio is in the watch tower when the hillbillies set fire to it. Realizing their fate if they stay, the three then jump out the window and onto nearby tree branches in order to escape the blaze. After escaping the towering inferno, it seems that the fire dies immediately. These three don't go far after jumping and are in the trees for some time. Shouldn't there be a great glow and lots of noise and smoke from the fire as the watch tower burns down? (00:53:45 - 00:56:00)
Plot hole: In the institute, Will's friend gets out of his room to get the guard's keys. He couldn't have gotten out of his room because there isn't a handle or door lock inside the room.
Plot hole: Why would Madison Lee put the bomb in the car if she was so convinced that the Angels were dead? If she wanted to off them just in case, she could have shot them while they were unconscious. (01:21:50)
Plot hole: The suitcase with all the money is at the fake doctor guy. This makes absolutely no sense - it was given to the girl. Why would she hand it over to that guy when they could have done the splitting of the money right that night?
Plot hole: When Bryan is shuffled in at "The Baywatch" as one of the dancing extras, wouldn't the director of the film notice that one of his beach dancers (Bryan) is actually dressed for cold weather rather than a day at the beach? He's wearing sweats and a hooded sweatshirt, and he stands out like a sore thumb with all those girls in bikinis around him.
Plot hole: A tsunami has supposedly just hit the island, yet the trees and plants (and a 500 year old treasure chest) are undamaged.
Plot hole: When the "black diamond" is being turned into its dangerous form, the arms dealers get very excited. Yet all they actually see is a very pretty laser show. There is nothing to show that the object really has any destructive power. Arms dealers make their fortunes by being cautious and smart. They shouldn't be so quick to accept the claims of the bad guy and bid money on possibly useless stones. (01:18:20)
Plot hole: What on earth are those sailors doing with Hyde when he is chained up on The Nautilus? He is solidly chained to the floor and walls and they keep stepping up to him to allow him to swat them out of the way, risking injury or even death. They stand around like idiots as if waiting their turn to walk up to Hyde and be belted across the room. Why? Why are they even there? Hyde doesn't need subduing, and if he needed guarding they could do it without getting into range.
Suggested correction: They are there to subdue him because he is strong enough to tear the chains from the walls, which he does seconds after they stop trying.
Plot hole: When Qiu is leaving Emilien, she ties him to a chair, sitting on a raised platform. This is to make it possible for the big ball to hit Emilien. But, when Daniel arrives, Emilien is able to throw himself into the trunk, which means, that if Daniel didn't show up, Emilien could have just thrown himself to the floor instead. So if he would be off the raised platform, he would never have been hit by the big ball in the first place.
Plot hole: Calden would almost certainly not be allowed into the autopsy room without some protection: a facemask, goggles, gloves. Not only to protect from errant bodily fluids (as we saw) but also to protect from any infectious diseases those fluids (or any escaping gasses) might carry. Also, he runs the risk of contaminating the evidence.
Plot hole: It's amazing that the two Chapman women weren't caught at "Rock for Daddy Day Care". One of them unzips a guy's dog costume in the middle of the path with everyone walking by. A little kid actually stares right at her when she does this. Also when Jenny puts the cockroaches in the salad, the people who were waiting in line for food would definitely have seen her. There are many more parts like this.
Plot hole: Throughout the film, anybody who speaks English uses Modern English, with either a British or French accent as appropriate. However, 1357 was solidly in the Middle English period. Although that language would not be utterly incomprehensible to modern-day travellers, neither would it be indistinguishable as it was in the film. The film specifically draws the viewer's attention to language at several points, making suspension of disbelief impossible. The French speak French, and very few of them speak English. There is a scene in which Andre is talking to Claire, and her lack of knowledge of modern idioms makes the conversation difficult; that should be true for all characters at all times. If the historical people were talking alone among themselves, I could accept that they're being "translated" for us. But they're talking directly to the modern travellers - it's too jarring.
Plot hole: When the innkeeper is asked by the rich ex-actress to give her the key to a nice room, he gives her a key telling her that eight is cozy and the key has an 8 on it as well. But a few minutes later, when this woman is about to be murdered, she leaves her room (holding her mobile phone) and the door has a 9 on it. How can a key to the room 8 open the door of the room 9? [Still a mistake, but there's an explanation. In the DVD extras you can see a deleted scene in which she changes rooms because she wasn't happy with 8.]
Suggested correction: This isn't a plot hole. It's just your unfounded assumption. There's no evidence to support the supposition that the T-X has such audio detection capability.
Even if she could detect it, how could she discriminate between the sound of Catherine breathing and that of the dozens of caged animals in the room? That's stretching even fictional technology a little far.