Continuity mistake: Almost at the end of the movie, Warden Ranken is trying to board the train hanging from a ladder of a helicopter, and Manny is yelling to him through the right windshield of the second locomotive, the old F7 streamliner. If you look closely when the camera shoots from the inside of the loco and forward through the windshield, you will see that the first engine is gone.
Continuity mistake: After the accident with the caboose, we see some inside shots of the first locomotive showing lots of debris from the caboose having penetrated the windshield. But in the outside shots, you can see that there are lots of debris on the front of it, but the windshield is intact.
Continuity mistake: After colliding with the tail end of the freight train, Manny looks forward along the right side of the runaway train and announces that all the hand rails are gone (torn off in the collision), yet for the rest of the film, all the hand rails on the right side of the locomotives are present and undamaged. The left side of the train (the side that has much more contact with the freight train in the collision) is never seen again in the film, presumably to suggest that is the side that lost its railings, which explains the twisted railing debris between the locomotives seen when the characters are moving between them (along the right sides).
Continuity mistake: When Manny first sees the train they're going to board, they walk a short distance alongside the train as it's moving. Pay attention, and you will see that the second locomotive, the F7, is missing. The first locomotive is now coupled to the third locomotive, even though the F7 was there in the shot before and is back in the next shot.
Continuity mistake: Towards the end of the film, in the control room, as the guys are arguing about what to do, the man sitting at the computer terminal is wearing a sweater over his shirt and a black watch. The older man says something, then goes over to the terminal, but now the guy's sweater is off and his watch is in front of him on the desk.
Continuity mistake: When Warden Ranken first goes to see Manny in his cell, he is walking down a prison corridor with prison cells on the left side of the camera and the prison wall on the other side. And when he is coming back from Manny's cell, he is coming down the same corridor. The problem is only that he is going the same direction as he was when he was going TO Manny's cell.