Vassal levies raised too long, but where?
Solution 1:
The opinion penalty for raised levies ticks down by 1 point every X days (currently 61, may be different across patches) after dismissing troops, just as they tick up every X for having raised troops. Thus the penalty and notification will remain for some time even after dismissing your vassal's troops.
Additionally, though this may not be the case here, ships count as raised levies as well. I've forgotten about some fleets off in some corner of the map before, leading to some hilariously high penalties.