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.
Character mistake: Engine #1206 is instructed to take the nearest siding upon hearing the news of the oncoming train. Frank does the maths and determines that they will not fit into that siding. He states the siding being 4011 feet between signals, with about 2500 of actual usable space. Engine #1206 with 25 cars would only equal 1580 feet, giving them more than enough room to clear in the first available siding.The average length of a railroad car is 60 feet. Even if the cars were considered "long", total 25 cars would have fit into that siding.
Factual error: The vigilance system on the locomotive, once unattended for at least a few minutes, would apply the brakes (which in the movie said wouldn't work, which is true) however it would also cut the throttle automatically, so the train wouldn't accelerate.
Continuity mistake: When Dewey and Gilleece are in the rail roller truck, the tailgate of the truck is clean with nothing on it. After the attempt to climb on 777 fails and the door gets smashed off, the tailgate suddenly has some kind of equipment either attached to or exposed off the tailgate in the middle.
Visible crew/equipment: After the train crashes into the horse trailer, there is a scene with Denzel's train talking to dispatch. They are talking about how Denzel's train is too big to fit in one of the sidings. During this scene, the camera is moving around the train looking through the cabin. The head of a crew member is visible reflected in the glass.
Visible crew/equipment: When 7375 and 7376 pull out of the siding in the attempt to slow down 777, Judd Stewart is the only engineer controlling to two engines, he is sat in the front engine (7375). However, when the camera is on the second engine, 7376, a person can be shown sat in the cab of 7376.
Continuity mistake: Near the beginning of the movie, we learn from Dewey talking to Connie that train 777 is pulling 39 cars. At the end of the movie, we see a front view of 777 stopped on the tracks. The tracks extending back from the locomotive curve off to the right and you can see the rail cars all the way back to the blue locomotive 1206. There is nowhere close to 39 cars between locomotive 777 and locomotive 1206.
Continuity mistake: When the truck with the horse trailer is across the crossing, 777 is way off in the distance with a deer crossing the tracks. The next shot of 777 shows the train a lot closer to the crossing and then in the final shot, it shows 777 way in the distance again, showing the same deer crossing the tracks.
Plot hole: When they try to slow the runaway train using another train, the lead train slows to 40 mph but after the failed attempt by the military veteran to board the train, the lead train begins to increase in speed, eventually being derailed. The failed attempt and subsequent injury to the military veteran, although disappointing, would not have caused the runaway train to miraculously speed up, especially since the lead train was already capable of slowing down the runaway train down. (00:41:58 - 00:46:00)
Character mistake: In the reporting of the scene where the Pennsylvania police shoot at the train trying to hit the red button that would stop the train, the report said they were firing shotguns. They were firing M16 rifles.
Suggested correction: Not necessarily. Some engines may not have a rear cab access (like Frank/Will's engine had). And even if the rescue engine did have a rear cab access 777's engine only had a side access stair which at the speed it was going is more difficult to climb over from the engine in front of it.
Actually 777's catwalk goes across the front, from side stair to side stair, but someone would have to leap over a rail or a chain to get onto it from the other engine. Why would there be stairs on the right side unless there was a catwalk to get to the door on the left side?