!!POSSIBLE SOLUTION!! Alpha 21
VIDEO EXPLINATION -
I has this issue with multiple clear/infested quest i was flying around looking for zombies i ran the whole monument several times and still no luck but i read somewhere that buttons can be triggers for zombies spawns and not pressing these buttons would result in the quest no being completed.
However some of the buttons that are clearly meant to be pressed, even the final vault door just simply could not be pressed, (no green light on button, it was just off) now i dont know what causes these buttons to not be active.
A simple solution you can attempt during the clear of any POI is to make sure any button you passed is pressed and if you cannot press this button due to it not spawning on breaking the button will have the same outcome as pressing it. (buttons do have 7000 HP but at a higher level this takes no time at all).
I hope this can help even 1 person but if you still have issues please comment on the video linked above and we can have a discussion there and finally sort out this issue many many players seam to be having.