It has been some time since I had a purge on my main single player character (currently have it disabled) so I don’t know if this will work or not, but I did have a few instances where the purge glitched out and “started” but I wasn’t notified nor did it actually commence. To fix it, I would go into the server settings and disable the purge and then back out of the server settings and play the game for a bit. I would then usually get a message that “(purge type) have been defeated”. Then I would go back into the server settings and reenable purges and they would begin to work normally again. This will probably reset your purge meter to zero though.
Another thing to look into regarding the location of your base. I have a large base on the mountains near the Black Hand Camp called The Pocket (upper left corner of 7H). I had lots of issues with purges spawning thralls inside the mesh of the surrounding landscape as my base is on the top of the plateau. I don’t know if this was causing the purges to bug out or not but if you get a purge and can’t seem to find any purge NPC’s, activating ghosting in the admin menu may help you to find and eliminate them and keep the purge going through its natural progression. In my experiences, if the purge is interrupted from completing I would get something similar to what you are experiencing.
Hope this helps you out and good luck.