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 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: 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: 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: 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)