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: At the beginning, it shows Santiago crossing the border into the U.S. But the U.S. border patrol is on the Mexican side.
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: The movie takes place before and around 1938 and, supposedly ends in that year, following the entrance in Shanghai of the Japanese, with the exodus by many Chinese and foreign residents. Ralph Fiennes' character, as an American ex-diplomat and businessman, would have resided, have bank accounts, his car, etcetera, in the foreign concessions. The Japanese did not occupy the concessions until after Pearl Harbor, so there was no need for him to flee the city, as a refugee without a passport and with little or no money, sailing towards Macao in a fragile Chinese junk. He could just have driven or walked a few blocks to any of the "Western" concessions, from where he could have married Natasha Richardson's character, obtained U.S. passports (White Russians had none, as the rest of her family in the movie until assisted by an official in the French Consulate) for her and her daughter, purchased a ticket in a safer vessel, sold his assets (regardless of the damage to his club, he still had a house, furniture, a car, presumably bank accounts, etc.).
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: 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: 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: When Pumpkin is telling Sayuri about Hatsumomo talking to Dr. Crab, she says that she was waiting outside during the conversation, and while she could hear it, she couldn't see them. However, at one point Pumpkin describes a facial expression of Dr. Crab.