The same issue started for me with mod version 2.4.0, seemed like it was fixed in 2.4.1, and the issue came back in 2.4.2. The temporary stop gets deleted immediately after the train reaches it (not sure if that's how it worked before, i havent double checked) but as soon as the temp location is gone the train heads to a different station.
I have rolled back to mod version 2.3.4 and its working again for me with my current save.
Edit: Nvm, still an issue for me