Plot hole: If Jack can speed the train up, why does he not try to slow it down? Even if it can't be stopped completely, using the speed lever to reduce it to the minimum possible would be a sensible course of action. There is nothing to suggest he wouldn't be able to do this as he is able to increase the speed without any trouble. If there was something to show that slowing down the train would be unworkable it would make sense, but seems to more serve as a plot device.
Plot hole: Payne's finger prints would've been all over the elevator, on his shotgun, and near the area where he killed the security guard as he was never shown wearing gloves. Since he was a former police officer, I would assume his prints would've been on file with the FBI and in a multitude of databases. You would think they would've been able to identify him much earlier in the movie than they did by running the prints through all databases of finger prints.