Pausing and unpausing the train fixes it every time. No other manual intervention is required.

Interestingly the rail blocks directly south of the train have all yellow signs.
My idea would be that the train planned to go south but didn't? => trainpathing "crashed"? That would also explain why i also had two traincrashes, what shouldn't be possible with the logic behind blocks.
Savegame and used mods:
https://www.dropbox.com/sh/t3embnr4wcwe ... u041a?dl=0
*Edit: the yellow signs disappear the instance i hit the pause train button.
**edit: added version to title