Look here:
http://www.gametrailers.com/video/e3-09-alpha-protocol/50419
Skip forward to about 1:20 for the relevant scene.
They get distracted by a sound while in patrol mode, and suddenly they focus so much on finding the source that they completely blank out everything around them? Sorry, maybe it's just me but that's not normal. They're not under assault, they're not in mortal danger, so there's little in terms of pressure to distract them so heavily. Yet they don't realize they're on the train track, and don't hear the sound that signals that a train is coming. It's hard to excuse this in any way.
I didn't really mean it to excuse that part, I just thought I'd point it out, that's why the sentence started with 'by the way'.