I had a bug similar to this with the Institute's Pest Control: Croup Manor quest.
I had cleared the settlement out just before I got the quest from the Institute and made it one of my settlements.
But every time I came back there were dead bodies of the original ghouls I killed there. They were stuck in the roof and floor of some buildings. I threw them all away and every time I came back, there they were.
I couldn't get this to work at all. The ghouls I needed to kill for the Pest Control quest were already dead. And the game doesn't respawn them.
Eventually I found a forum post where a guy killed all the settlers to fix it.
I hated to do it, but I saved the game, then killed all the settles.
My Pest Control Radiant quest was finished and it still works as one of my 5 radiant quests.
So try that Save your game. Then kill all your settlers. New ones come as long as you have the radio tower set up. And it fixes that Pest Control bug.
Sadly it does nothing about the reoccurring ghoul dead bodies coming back every time.