The train they collided with was an eastbound train which 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.
Eastbound 12, the freight train whose caboose is hit by the runaway, is initially being pulled by a pair of GP40-2 locomotives. But they are then switched before the collision to a pair of ALCO MRS-1 locomotives, led by #1605. The consist also changes, from blue hopper cars to a mix of flat and box cars.
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 the prison guard from the helicopter falls off the train after crashing through the window, his goggles are missing and his face is covered with blood. In the next shot, showing him getting run over by the train, he is wearing the goggles and the blood on his face has disappeared.
As the runaway train passes by Pulasky's post it is clearly visible that there is almost no snow around the tracks. In the next shot, which shows the locomotive's burning brakes and Pulasky's attempt to lift a hot piece of debris from the brakes, the ground is covered with deep snow.
In the yard sequence, where Manny and Buck walk beside the train before boarding the last locomotive, the second locomotive is missing. In clear view the lead engine is attached to a GP7, although a shot seconds before shows all four locomotives.
The close-up shots of Manny's grip on the coupling show him holding on by just his finger tips, but in the longer shots the positioning of the fingers is different and you see that his whole hand is on top of the coupling.
In the sequence where the train runs through a series of tunnels there is a montage of shots of Manny yelling at Ranken out the front window of the second locomotive. In these shots the rear of the lead engine doesn't feature. It should be dominating the view forwards, but is nowhere to be seen.
When the train emerges from the tunnel portal just before the bridge, the portal looks completely different from the way it looked in the preceding shots showing the police waiting for it to emerge. The latter shots show a continuous pale concrete structure, but by the time the train emerges this has changes to a brick structure consisting of stripes of varying yellow and grey hues.
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.
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.
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 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.
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.
Following the collision with the freight train, a long shot shows the runaway passing as debris rains down on and around it. As the third locomotive passes, a truck from the caboose bounces off the top, then bounces off the cab of the fourth locomotive without causing any damage. Such collision would have ripped open the cab of the fourth locomotive. The crash was filmed using scale models, which didn't sustain damage the way real locomotives would have.