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: 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: 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: How did a woman who had just escaped from a mental institution get out of the country so fast? Even if she had a passport already, she wouldn't have it - the hospital or her family would. How could she get it back from them without SOMEONE turning her back in to the institution? It takes a lot to get involuntarily committed in the US, and I doubt she could get un-committed that fast, even with the guy she tried to kill vouching for her.
Plot hole: Why did Inspector Gadget put his glove on his right hand? We see a toilet brush in place of his hand with a glove on it, yet when he's flying through the air doused in toilet water, he has his glove back on.
Plot hole: In the shot where two of the pirates find Jack Sparrow in the prison, you see the moon shine out over Port Royal and the pirate's hand around Jack's neck is skeletal. While this is happening we know that Elizabeth is being led onto the Black Pearl by two pirates. If the pirate in the prison turns skeletal, why don't the pirates with Elizabeth turn skeletal? It's clear that they don't as Elizabeth only discovers the curse later on aboard the Black Pearl.
Suggested correction: This can be explained that on the route from Elizabeth's house to the ship there is a lot of fog, smoke from fires and gunpowder explosions, so the moon doesn't get through. The moon only get through once they are underway again and the fog is cleared. The prison is much further and higher than the town and so the moon does get through (only sometimes) there.
You're very much mistaken. In later scene pirates turn skeletal when marching underwater, at the bottom of the ocean. Moon is easily able to get through water and this smoke isn't thick enough to block the moon.
How does water compare to fog? Of course the moonlight comes through the water, its transparent. Fog isn't transparent. You can go technical and question how much the moonlight is reflected away before the effect wears off, but obviously the effect wears off when there is no direct moonlight hitting them, as is the case with fog and smoke.
Plot hole: Singe states that Viktor and Amelia are pure-blooded Vampires, and seems to agree when Viktor calls the story of the Corvinus Clan a legend. However, Evolution shows that Lucian had formed a partnership with Andreas Tanis, a Vampire who was outcast by Viktor specifically because he knew the truth of the Corvinus Clan and the origins of the Vampire and Lycan bloodlines. Given his lack of loyalty to the Vampires, there is no reason why Tanis would not have told Lucian that Viktor and Amelia are not pure-bloods, or that the legend of the Corvinus clan was entirely true. Lucian would have passed this information to Singe, as it would be vital to his work.
Plot hole: When the plane is trying to land on the bridge, it hardly makes it. How do they rotate it 90 degrees? The plane wouldn't fit.
Plot hole: When we first see Lara in her wetsuit, she has a back pack attached to her harness, a torch on her left shoulder, some sort of pistol-thing on her thigh, her 5-barrel dart gun by her left buttock and a little pouch in the small of her back. In the temple she takes off the pistol-thing, dart gun and backpack, yet after climbing the statue manages to produce a video camera, safety spectacles and a cutting/welding device from somewhere.
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.