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: Toward the end of the movie, it is revealed that Silvia spent the night in the secure room where the Matabo President was taken after the assassination attempt so that she could be alone with him and threaten to kill him. With the U.N. and Secret Service on alert for an assassination attempt, wouldn't they have swept the secure room right before the Matabo President arrived that day? In addition, Silvia would have had to use her access card to get in that area of the building, so there would be a record of her being in the building but not at her station. Wouldn't that raise some suspicion long before Tobin figures it out?
Plot hole: In the end, when Charlie is advancing on Emily while turning his light on and off, the final time he turns it on, Kathrine is in front of Emily. How could she get there so fast without being heard? There's at least 4-5 inches of water that would make sneaking very hard.
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: 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: During the end of the fight scene in the hotel, Charlie gets hold of Dexter's gun. This gun is a Desert Eagle variant that fires either a .357, .44, or a .50AE caliber round. At the close proximity to Laroche that Charlie was, he would have taken his head clean off his shoulders instead of just taking out his eye.
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: In the scene where The Commander and Jetstream are called to fight the giant robot, Will's mom says "What if he forgets his lunch?" In every scene where he's eating lunch at school, Will has a school lunch.
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: To taunt Agent Augustus Eugene Gibbons, General George Deckert namedrops Darius Stone. Gibbons looks at him genuinely shocked, which the General acknowledges scoring an important moral victory and establishing himself further as a Machiavellian villain. The problem with all this is that Gibbons would have to literally not know what he's been doing and why up to that point, to think that the General, who is also the Secretary of Defense, does not know about it.Gibbons broke Darius out very openly, from a military prison that is the only maximum security correctional facility in the Department of Defense. His reason to bring Darius out was also, explicitly, that Deckert is targeting the ex members of their unit (which is, we have to assume in retrospect giving perhaps too much credit to the screenplay, the only reason why Gibbons could execute such a flawed plan to begin with and why Darius is still alive). So, Gibbons being surprised that his adversary "knows", after a couple of days even, is pure absurdity.
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: Lisa calls Cynthia and tells her to pull the hotel's fire alarm, which she does. Cynthia then physically goes up to the Keefe's suite to warn them something is wrong. Even though the fire alarm was pulled and it can be heard blaring in the lobby, the Keefes and the security team seem to have no idea that there is a problem until Cynthia knocks on the door and tells them to get out.