Deliberate mistake: The entire plot wouldn't exist without this one, but just before the engineer stumbles out the door and falls off, he pulls the big red lever on the left side of the cab. In the real world this puts the air brake system into its emergency mode. Among other things, this mode trips a solenoid which causes the engine to return to idle, and the electrical system to not put out power. Neither the Diesel engine nor the electrical system will respond to control inputs until/unless the air system is reset.

Runaway Train (1985)
1 deliberate mistake - chronological order
Directed by: Andrey Konchalovskiy
Starring: Jon Voight, Eric Roberts, Rebecca De Mornay, Kyle T. Heffner
Continuity mistake: When you first see the freight train that eventually would get its caboose smashed, the locomotive is a big one with lots of snow on the front. In all the other shots of this train, it`s a smaller locomotive, and it has no snow on the front.
Manny: You do what you have to do, I'll do what I have to do. Whatever happens, happens.
Trivia: This is, the way I see it, a VERY serious mistake by the filming crew of the movie. The Alaska Railroad, where the shooting of the movie took place, wanted all their logos and paint schemes of all the trains in the movie to be camouflaged. But yet, on the first shot of the locomotive of Eastbound 12 (yes, that is the shot of it before it mysteriously changes from ONE GP40 to TWO ALCo MRS's), you can see the blue and yellow paint scheme of the Alaska Railroad. On the DVD you might even be able to see the printed ALASKA on the side of the loco.
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Chosen answer: Most likely from the speed at which the train was going, a train is like driving any large vehicle. You have to maintain a certain pace, to stop at an instant, for the unexpected.