This happened to my in the Campaing, 2nd map.
I had the main hero, the priest from the temple and the murderer-type fighter. After reloading in the middle of the map the other 2 heroes (but not my souvereign) were cloned. After reloading an older save they cloned AGAIN, so there were 3 of them.
I didn't restart the game and then loaded the campaign savegame yet. This hasn't happened in a regular sandbox game yet (and I have played quite a bit of that).