Just had this bug happen to me again. Got a minuteman radiant for County Crossing. Left Dunwich Borers to go to CC; quest to clear nearby training yard. Did so, and got the settlement available. Went to Finch Farm to make a Settlement Creation Kit, and got a popup that Abraham Finch is now leader of Sanctuary, which was previously Sturges. Finch was being built with the RotC plan, and was pretty close to going to level 1 from level 0. Rebuilt the local data; no leader now. Assigned Abigail Finch as leader and had to restart the city from ground up (fortunately, it's rebuilding fast).
Went to Sanctuary, and sure enough, Abraham was listed as the city leader there. Rebuilt the data, which didn't remove him, so I just reassigned Sturges.
ETA: When I built the desk at CC, it showed Professor Goodfeels as leader (he was leader in Sunshine Co-op). I hadn't done anything at CC yet but build the desk. I guess when I go to Sunshine now, it's progress will be borked (it was at level 1). <sigh>
ETA #2: Yup, Sunshine is borked; had McReady as leader, even though I just assigned him to CC. Restored Goodfeels, had to rebuild the settlement. I'm beginning to think all my RotC settlements are borked now.
Hope this helps provide a bit more detail for your bug hunting...