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: 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: 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: 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: Just before Cowboy finally opens the bowling bag, the zipper is halfway up the right side. John was warned not to open the bag and was terrified by the potential consequences; he didn't open the bag at any point and certainly wouldn't have allowed it to remain partially open. (01:13:30)
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.