In playing scenarios I have frequently had trouble with pathfinding as others obviously have too and usually a waypoint on the correct track will suffice. Occasionally however the train still stubbornly goes the wrong way, often in this kind of example where a freight train or similar passes through a station and is meant to take a particular route. One solution I found that sometimes works is to put an additional waypoint before the station, thereby bringing the route in line with the correct track at the junction - ie in this case making waypoint 2 lead to waypoint 3 (I think the dashed lines you can see between stops/waypoints are to give you an idea of where the train should be heading in a direct sense.)
I hope this is useful to some people, I know it can get a bit frustrating if you can’t find a way to send the train the right way.
