I had the situation when I built a fungal bloom on a pacified village, but it seems that before the construction is complete the AI Cultist converted that same village, so they could still spawn minions out of it. In order to destroy it I had to first destroy my fungal bloom and then I was able to destroy the cultist's village.

I am sorry, initially I overlooked this fact so I didn't keep the save file. I just would like to know if this mechanic is intended or not.

I will try to play another game that has this situation.

EDIT1: I just found out using the the command attack on the Actions windows you can destroy the village without removing the fungal bloom. Still would like to know if it is working as inteded

And another village in the same region:

EDIT2: Found the savefile

Mykara - Turn 81.sav