I seem to remember something about this... IIRC it happened when a leader moved into Harpers Ferry alone and entered the city, and the leader was targeted by a friendly, moving stack. Once the leader has entered the city, but before the targeting stack has caught up to and merged with it, an enemy stack enters the region and captures it, which kind of locks the leader inside the city--hey, I wouldn't be marching down Main Street in that case either
Because all stack in the region are then in DP and everybody has => 5% MC no battle ensues when the stack targeting the leader enters the region and merges with the leader stack, which is now inside the city.
As has been noted, you can still select the leader's stack though the <F1> unit list and can be issued order normally.
It seems Harpers Ferry is the only place I've seen this happen, which may have to do with the configuration of MC and loyalty and the simple fact the everybody is racing to take control of it at the same time