Continuity mistake: The caboose and troop cars were decoupled. Later, after Rev. Peabody disappears, the train is shown chugging along with all the cars. (00:55:00)
Continuity mistake: When the fireman falls from the engine passing over the deep gorge we hear him screaming. John Deakin examines the body and later explains that due to the lack of bleeding the man was already dead before he fell. (He theorizes he was killed and then pushed from the engine because he had discovered the 2 bodies of the missing officers in the woodpile).
Continuity mistake: When John Deakin discovers the Reverend's body in the coffin, the Reverend's eyes are closed in one shot and open in the next.
Revealing mistake: The caboose and two bunk cars are uncoupled and sent rolling down the hill, with troops locked inside. As the cars roll off a cliff, troops can be heard yelling. However, as the cars hit the ground and shatter into rubble, the wood does not appear to be blood stained, nor does there appear to be any sign of bodies in the debris. The cars were obviously empty for the scene, and given the circumstances of the soldiers allegedly trapped within them, it's unlikely that any of the soldiers could've gotten out in time.
Factual error: All the couples on the train are modern and not correct for the period. Trackwork back then wasn't very good, considering the speed that the back end of the train is going it probably would have derailed long before it did. The caboose and the rest of the train seen to be just shunted off the track for the dramatic crash, realistically it would have flipped over and gone over the trestle.
Audio problem: In the scene just before the engineer falls from the train, all the main characters are gathered in the governor's car. Charles Bronson is pouring alcohol from a decanter. The "glug, glug" sound of pouring begins before the actual pouring starts.
Answer: Ben Johnson and Charles During. Their characters had guns pointed at them, they stopped the train suddenly to knock them off balance. As soon as Bronson and the Major jumped off the train, Johnson and During took control of the engine.