I don't know if it's a bug, an omission or me playing badly, but here's the deal :

1. I declare war to the orange team, who is allied to the purple team. I am allied with the green team. 

2. I conquer the purple territories but in the same time, the green team take the purple team as vassal as I keep on the war against orange team.

3. After the war, orange team becomes MY vassal, while the purple team was already the greens's vassal. So we are all allies, at peace and stuff.

4. BUT all the purple cities I conquered remained "occupied cities" (occupied by me) with 0% stability, keeping spawning rebel units. I can't build in them, I can't liberate them, I can't give them, ransack them, absorb them, I can do nothing. Nobody seems mad at me about this, it's just an occupied territory in the middle of the continent, spawning rebels. It looks like I created some kind of ISIS situation. 

After that, I broke the alliance with the green team to see if something would change, but it didn't. 

Did I miss something? 

Or was the diplomatic situation too complicated and unexpected for the game?