Plot hole: Had one or more locomotives coupled onto the real runaway's front engine, or even just been pushed by it, anyone aboard the "rescue" engine could have just walked to the unoccupied ones and shut them down - no copters or fireballs required.
Continuity mistake: In the scene when Train 777 is coming straight at the passenger train with the kids, the train is coming straight at them (just a single track). But a few shots later, a rip track leading to a siding comes out of nowhere without being seen. (00:23:05)
Factual error: In the yard when the air hoses are discovered to be not connected, the purpose of the connected hoses is to release the brakes, not apply them. With the hoses disconnected the brakes on all the cars are automatically applied.