Plot hole: Now why the heck is one of the stealth fighters anywhere near the train? Stealth fighters use advanced targeting and do not need to be anywhere near their target, yet in the movie the one fighter is so close to the train when it gets blown up that it looks like it's on a collision course.
Plot hole: When Casey determines to hot-wire the Chevy truck, he raises the hood, grabs two bare wires on the passenger side of the engine, rubs them together, and the truck starts. However, this is patently impossible since the ignition is in the off position. The engine might crank, assuming he magically found the hot lead to the starter solenoid, but it would not start.
Plot hole: Dane says as long as the train is moving the signal to Grazer-1 is completely transparent. So shouldn't ATAC have been able to find Grazer-1 during the ten or so minutes the train was stopped while the bad guys were looking for the CD?
Plot hole: At the end of the movie once Ryback and the others take over the helicopter, Ryback calls in to ATAC to let them know the hostages were OK. How did he manage to do this? He didn't know where Admiral Bates and his people would be, only that he was able to send his fax message to his cafe, which still had no idea if his message got to Bates at all. It also begs the question how Ryback could turn a dial on a radio and magically call in to a top secret military facility that he didn't even know about.