My friend and I have similar issues with clears, at least for tier 2, 3, and 4 quests. We clear the poi and the quest isn't updated to reflect that. We go through the poi multiple times to look for rooms/areas that we've missed, and the quest still isn't updated. Last night, I think we were down to one zombie and the yellow marker showed the zombie above us in the underground area but below us up top. I think it might have gotten stuck in limbo between two areas. I tried digging to find the zombie, but to no avail.
We've noticed in the past two weeks that the zombies spawn in late when doing clear quests; like, after we've walked through and looted several rooms, we have a multitude of zombies appear in the rooms that we just walked through. We can run the same poi as a fetch quest and don't have any issues with zombies loading, the issue only happens with clears or fetch/clears. So, it appears that this phenomenon only occurs when the player has to clear the poi; whether it is a fetch/clear or a straight up clear. Whenever possible, my friend and I choose buried supplies or fetch quests over clears because of this issue; however, the clear quests are unavoidable in the higher tiers.
The command, "sleeperreset" seems to work; however, it resets sleepers everywhere, including our home bases.
I know I read a new thread somewhere in which a person encountered a similar issue. They deleted the Data/Prefabs folder and validated the files, but it didn't work. They were also advised to use the "chunkreset cr" command, which didn't work for them or for us.
We will try deleting Data/Prefabs folder and let Steam reload it and validate, and let you know how it works for us.
The same/similar bug has been reported and I think that I read somewhere that it was "under review."