Plot hole: The whole concept of a kidnapper 'pretending' his victim didn't get on the plane in the first place is utterly laughable. Even if nobody saw her in her seat, why didn't they see her walking down the aisle to her seat, or waiting to board the plane, or in the boarding tunnel itself? Why isn't she listed on the passenger manifest, or on her mother's travel documents or airline ticket? And there would have been security cameras all over the airport.
Plot hole: After the bird is hurt, Jimmy is shot several times and wounded very badly. Yet just seconds later, he is able to save the young boy, and mysteriously use many of his "crow powers" despite being hurt very badly.
Plot hole: The survivors find their way to the internet lounge to send out a message via email about the terrorist attack. The ship was upside down. All satellite dishes used to transmit over the internet were completely submerged in water. Even if there was power to the computers, they would not have been able to get a server connection let alone send out email.
Plot hole: There is no way Dirk, Al, and Eva could have made it from the top of the fort to their camels, raced cross the desert and then hid themselves in the sand all before the train were to have met them. The train was barely visible when Dirk saw it through the scope which means it was much farther away to begin with.
Plot hole: At the start of the gun fight at the house, a snowball is thrown at Jack who then follows the person into the street. When they turn around the person is wearing a hockey mask and Jack realises he's in trouble. Jack would've seen the person wearing the hockey mask when the snowball was thrown, as the person had to be facing him to throw it. There was no reason after that for Jack to follow him.
Plot hole: In the opening text scroll, it is said that the creatures live in the dark, and the name of the movie is "Alone in the Dark". But at the very end (when Edward and Aline are walking around the deserted city), the camera zooms in on the couple suddenly, implied they were attacked by one of the monsters, but in broad daylight.
Plot hole: When the group first finds the plane, they are all able to hold their breath long enough to descend, search the plane and resurface. Yet later in the movie, even though Amanda can get a full breath of air from the air pocket in the plane, she can't hold her breath long enough to swim to the surface and has to be rescued by Jared.
Plot hole: Tyler jumps into the water, then grabs his mask and puts it on and begins swimming, but he fails to clear his mask by blowing the water out of it. Without clearing it, he wouldn't have been able to see a thing.
Plot hole: Travis does the last time jump to change the events of a previous time jump. As all the jumps were to the exact same time to kill the same dinosaur, the travelers of the second jump must have found there the travelers of the first one. The travelers of the third jump must have found the travelers of the second and the first, and so on.
Plot hole: After E.D.I. goes rouge, Kara brings up his weapons list, which consists of 2 ThroatRippers, 2 ShockHammers, and 3 Blue Ferrets, so E.D.I. has 7 missiles. He fires two during the Russian dogfight, another two when he and Ben escape from Alaska, and another two at the Korean border - one of which is the last missile. That's 6. So where did the last missile go?
Plot hole: The manner in which the Microwave emitter is used to vaporize the city's water would not go as intended. Microwave emissions coming from a device located inside of a train that has a very metallic exterior will unavoidably be affected by the photoelectric effects resulting from any microwave beam that is focused at the water mains below the train from within it. A fork placed within a relatively low powered kitchen microwave would encounter a similar effect.
Plot hole: At the end, Hartigan races out to the Roark Farm to save Nancy, where he takes out two guards quietly, with a switchblade knife. As he dispatches the second guard, we see the ruthless cannibal killer Kevin just yards away, inside the house, reading. Hartigan then makes a blunder, starts rushing, and he is shot by a third guard. Hartigan kills the third and a fourth guard with two handgun shots. Obvious question: With three gunshots in rapid succession just outside the remote house, why didn't the hyper-alert and agile Kevin come out and rip Hartigan to shreds? No, the generic contention that "Kevin wasn't concerned with Roark's son" is not an answer. When Marv infiltrated and attacked the Roark compound (twice), Kevin immediately engaged Marv. In both instances, Kevin responded to attacks on the compound without even knowing who was attacking. But Kevin completely ignores Hartigan's attack, which seems like a plot hole.
Plot hole: Gibbons is presumed dead and is an NSA officer with no documents or anything, but in the space of a couple minutes from furious shootouts he's the man who orders everyone around, summoning Black Hawks and all sorts of military forces just like that - and supposedly the whole army in the vicinity is hostile and loyal to the bad guys, even. (01:21:40)
Plot hole: If the creatures are strong enough to simply burst through the walls, as shown at the end of the film, then the creature upstairs should not have been stopped by the small door that Bozo, the bartender and heroine shut on it to stop it. It was one of the larger creatures as well, so it could have easily gotten through.
Plot hole: When the brakes fail on the truck, Cold insists that he and the woman have to jump from the truck, simply switching off the engine would have been effective seeing as the truck was a long way from crashing into the tanker, and plenty of room either side of it to avoid it.