I've noticed two variations of armies sharing the same tile, without merging.

1. a champion ends his journey (depletes movement points) on the same tile as my sovereign. My sovereign has movement points remaining. I try to attack using the champion. Result: Can't select champion until next turn.

2. I attack an enemy stack and win. Something happens (I don't know what) and the enemy is able to insert a stack under my own army. I have to move off the tile, then attack again, to re-claim my position.