Do you Sync your FTM file to an ancestery family tree?
This kind of bizarre behavior is sometimes reported by Sync users.
If that is the cause, the solution would be unlink the FTM file with the ancestry tree.
If Sync isn't your problem, do you do a lot of merges and then attempt to clean-up merges....?? This kind of bizarre behavior is sometimes a result of merging and attempted cleanups.
As for a solution, the only thing I can suggest is try to detach everyone that is in the "wrong" circle and re-attach all over again.