Rebelling units attack other units and core. Attacked units do not respond in any way and get angry themselves. Eventually they also rebel which keeps going on until all creatures rebel and destroy the core.
Suggestion 1 : Rebel units change their faction, thus become targetable by your creatures.
Suggestion 2 : Rebel units try to leave your dungeon through portal, if they can't, they start slowly lose health while keep attacking everything and everyone. Eventually they just die out of ''hunger''.