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: It doesn't make sense that Penn would shoot at the black suspension wires to break them off the train. His own men were originally on them to get to Ryback (who was barely hanging on the side of the cliff), and Penn never knew Ryback killed his men or that he was now the one now hanging on the wire.