If you have a train waiting at a wait stop with shapes actively coming in and you clear the contents from the shape loader (I hotkey), the train moves a tiny bit and ends up half-way off of the stop while remaining stopped. It seems like the train stops again the moment that the loader is "enabled" again by a single shape reaching it. If the train hadn't cleared the stop fully by the time the loader is available again, it stops regardless of it being past the correct alignment.