Continuity mistake: Multiple scenes: On every exterior shot of the train, you can only see one row of windows across the upper galley section. However, whenever there is a scene shot on the upper 'galley' level, there are two rows of windows, one right above the other. The external shots were filmed using a Chicago Metra train (which uses 'bilevel' galley cars), the internal scenes were filmed on a set in Montreal, Canada.
Continuity mistake: In the scene where the bomber shoots characters played by Jake Gyllenhaal and Michelle Monaghan, when filmed vertically, there's a splodge of blood in front of Michelle's face. However, when the camera is on the ground, filming her face, there's not even a vestige of blood on the floor when it should be exactly in front of her face.
Continuity mistake: When Colter fights the guy in the brown coat at the train station, the sun changes between shots.
Chosen answer: Trains that shuttle back and forth on shorter stretches don't usually turn around at the terminus. They simply go "backwards". So, in one direction the loco is in the front, on the way back it's at the end of the train.
Ioreth