Several places, on quests, I had to clear areas. Got the on screen prompt saying "area cleared"

One in particular...the Mayor's Bunker. Clear the inside. "Cleared Area" appears Go outside, go back in and find Glowing Ghoul and friends watitng just inside the door.

Hmmm... if that's the case, that svcks. This shouldn't be a loot-grinder with respawning enemies.