Currently on a newish play through (level 37) and having issues with settlements that think they are another. The first was Coastal Cottage, when i built a new desk there it didn't give me option to assign a leader, when I checked it thought the leader I had assigned to Tenpines Buff was its leader, and when I inspected the plan it thought it had Tenpines Buff plan. I 'change leader' and selected a new leader, travelled to Tenpines buff, and the leader there had also changed - and settlement plan thought it was Coastal Cottage. After a bit of testing I decided to ignore, and manual build Coastal Cottage. However, I have now just taken Somerville Place, and its done exactly same thing with Abernathy Farm.