Interesting. My natural suspicion is there's probably something happening with event ordering on a busy train network, as it relies heavily on events as for temporary stations the mod places stops in both directions (north and south or east and west), adds the north/east stop to the schedule and then tries to force a state change on the train. (I couldn't work out a better way tbh).
What should happen is either the train gets one of the "on the path" events (and therefore the north/east stop is valid and the south/west stop can be deleted), or the train gets one of the "no path" events, at which point it assumes its picked the wrong direction on a unidirectional track -- so it deletes the north/east stop, amends the trains schedule to the south/west stop and tries again. If its removed one of the two train stops, then its decided one of these two events has happened.
Some more info would be useful please, note by direction I mean the direction the train needs to be facing to arrive at the stop -- so an 'east' stop needs a train travelling right to left.
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Whether you're seeing this particularly in a north/east direction, a south/west direction, or an even mix of both. Basically I'm looking to see whether its decided it couldn't path when it actually could, it decided it could path when it can't, or a mix.
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Is this single player or multiplayer, is the train network one directional, bidirectional or a mix and a rough number of trains, to the nearest 100 or so (to get an idea of the number of train state events).
Other things that would be potentially useful is whether you know if the train being dispatched is more generally parked or already moving and whether you're seeing this more often closer to junctions than on clear stretches of straight rails.
I've had a play and can't find anything obvious, so I think it's likely to need some scale. If you have a consistent reproduction a save file would be easiest if you don't mind, otherwise I'll see what I can do with some of my older playthroughs, and look at adding some logging to a debug build to work out whats going on.