Used a custom sovereign playing as Pariden. Killed the caravan using auto resolve. Even though there was still movs left showing for the sovereign all it would do is create waypoints.
Saving, quitting then reloading (without going to the next turn) allows the soverign to move again (using the movement points that were left).
note: NOT using auto turn
note 2: happened twice on two different caravans (same faction though)
note 3: was at war with the caravans owner