Awfully sorry, but I am seeing a (new?) bug on a route with multiple waypoints.
Here is a saved game where I can reproduce this bug: http://files.simutrans.com/index.php/s/HTSbnzAUG7ifJq3
How to reproduce:
1. Load saved game.
2. Hit pause.
3 Jump to vehicle #14 (a stage coach) just a few tiles away from it's destination Croerbourne Monument.
4. Follow the vehicle, unpause and see the stage coach pull into the staging inn. First indication that something is wrong is that the stage coach will not go into the loading time counter but will immediately turn around and proceed to Wingburn Lacey, it's destination.
5. Please do not open the vehicle's schedule window now because that can cause the vehicle to proceed to the correct destination (but still via a wrong route, ignoring the wayponts).
6. Shortly before the stage coach reaches the city limit it will change it's destination from Wingburn Lacey to Croerbourne Monument, oddly enough at or near a tile with a waypoint.
Thank you for the report. This seems to stem from the current problem in identifying reversing stops/waypoints correctly. However, I have applied a fix which in my brief testing appears to prevent the particular problem described. I should be grateful if you could let me know whether this fixes the problem.
Thank you, James! With the new nightly build I have so far not seen vehicles ignoring waypoints, that looks promising!