Plot hole: Near the end, when Ice asks to say goodbye to the kids in the hotel room, the kids have on their pajamas, yet their luggage was left on the train earlier in the day. It is unlikely that they would have gone to the train station to get their belongings following the chaos of the Christmas party.
Suggested correction: They have backpacks so their pyjamas were probably in their bags.
In a scene right after the train scene the kids tell the mom that Nick lost their luggage. The mom may have picked up some pyjamas for the kids after learning that they lost their luggage.
Plot hole: In the end of the movie, when Willy Wonka decides to visit his father, his father does not recognize him until he looks at his "rare teeth." But the wall of newspaper printings that Charlie was looking at included a recent enough picture of Willy that the father would have definitely recognized him, before seeing his teeth, as Willy doesn't look like a normal person with that outfit.
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: 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: 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: 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: In the scene where Ann is laying/sleeping with Kong on the cliff, her dress should not only be beyond filthy, but it should be tattered and shredded. It doesn't so much as have a thread out of place after being carried so violently through the jungle and being caught between Kong and the dinosaur. Also, she at this point has been in Kong's possession for several hours to a day or so, and not once has she even shown any signs of hunger, thirst, or the need to relieve herself.
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: XXX and his ex (as redundant as it sounds) are learning from the TV the news of Gibbons' demise. He then tells Shavers "Let's get to work" and they plug the hard disk in, for the very first time because they realise that it's been wiped clean. It is night, and their mission was during broad daylight; if Gibbons had to wait nighttime to sneak into his own home, he could have easily helped them out during their mission, and it's absurd that they just sat on the crucial hard disk while chilling and watching the nightly news. Gibbons' house is billed as "Chevy Chase, Maryland", so it's just a few minutes away from their position. (00:31:00)
Plot hole: Even if Chicken Little was tagged out when he hit home plate, the game was already tied so his team would still have a chance to win the pennant.