After colliding with the caboose of eastbound 12, Manny looks forward along the right side of the 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.
When Manny goes to uncouple the lead locomotive from the rest of the train, he has a large wrench in his hand. When the camera cuts to the overhead shot just before Manny uncouples the locomotive, the wrench is gone.
When escaping from the prison, Manny and Buck wrap themselves in cling film. When they arrive at the rail yard and Buck takes off his shirt, it's clear that there is no cling film on his upper body.
During the helicopter shots where Rankin tries to put a man on the train, sky changes rapidly between sunny and overcast.
Before and while the train crosses the Seneca bridge, the words "Alaska Railroad" above the tunnel portal appear and disappear between shots.
Some have pointed out that the dead man's switch, a device intended for this exact situation, should have put on the brakes and stopped the train. Indeed it should have - however, it is explained in the film that the dead man's switch malfunctioned. Furthermore it has been pointed out that in a real situation the emergency brake application by the engineer would have switched the throttle to idle bringing the train to a stop. Although true, this shouldn't be considered a goof as factual accuracy would not allow further evolving of events.
When the ill-fated engineer notches out the throttle on the lead engine, the reverser handle (just below the throttle) can be seen in neutral.
The close-up shot of the engineer as he falls off the locomotive is flipped, creating a false impression that the engineer falls off the walkway opposite to the one he is actually seen falling off.
The dead end branch to which the train is sent to derail is supposed to be unused. However, look ahead shots show fresh tracks in the snow, so there must have been another train shortly before.
During the rail yard shots it is clearly visible that the last two locomotives (EMD GP7s) have Blomberg B type trucks. Later in the movie the trucks of the two locomotives change to AAR type B, which reveals that the locomotives are different. Yard shots were made at the BA&P Railway yard in Anaconda, Montana using local locomotives, which had Blomberg B trucks. Later filming was done on the Alaska Railroad, whose GP7s had AAR type B trucks. Furthermore, as the train starts accelerating in the yard, a close up of an AAR type B truck is shown, which reveals that the shot was made later in Alaska and not in Montana as the other yard shots.
The train they collided with was an eastbound train that was travelling in the opposite direction to them. But every time we see the map board in the control centre, their train is also going eastwards.
Manny states that the train's whistle did not blow prior to the collision with the caboose, yet a whistle is clearly heard as the runaway train is hurtling towards the junction.
Towards the end of the film, during one of the shots from under the speeding train, there's a crew member with a plastic bag throwing debris under the front of the train. At one point his hand becomes visible, and the bag is swinging from side to side.
Prior to the train crashing through the wall, we see a head-on view from the locomotive. Looking over to the right, you'll see a group of people (possibly the crew and cameraman) amassed by the wall, waiting to see this destructive stunt occur.
When they can't cross over from the A class stream liner to the lead unit and slow down the train Sara tells Manny and Buck that she knows how to stop the train, or at least slow it down. Manny then jumps to the lead unit and uncouples the other 3 units. However they could have uncoupled either of the last two units at any time, which would have then automatically shut down the train as shown in the last shot.