Do the Forgotten Masters prevent Full-Clear?

Hi guys,
I have had this problem twice in Upper Prison. Everything exterminated. Haku remaining after Mission. Get the info: "Monsters remaining: 1"

Searched everything twice. What a chore. Found nothing. What do you think?

Cheers,

T.

On maps like Upper prison bosses like Brutus counts as one of the remaining monsters on the map.

Same with maps with the bandits since the bandits count as monsters until you fight them so if you ally with any of them don't expect to clear the area.