I've been running long goods trains of a hundred wagons or more in the game, and have noticed that once a train gets beyond fifteen or twenty-ish wagons in length, there is a good chance that uncoupling the engine (for example to shunt or run around) can trigger a session-ending glitch. The issue appears to be that when uncoupling from a stationary line of trucks, compressed buffers can cause the trucks to jolt forward. On longer trains, this can add up to a considerable distance, and the resulting 'jolt' can slam into the engine with enough force to catapult it off the line. On other occasions, the glitch has shoved the train partially THROUGH the engine, resulting in Gordon or Thomas becoming fused with a Guard's Van! With Gordon the van formed a single unit with his cab and tender, making him look like some kind of articulated engine, while Thomas appeared to be cosplaying as Toby! The work-around solution I've found is to set sufficient handbrakes on the trucks before uncoupling to prevent them from jerking forward into the engine. Hope this proves of use. Cheers!
