I have the same thing at the red rocket garage near sanctuary. I sided with a certain organisation but there is a guy from the other main faction just stood under the overhang there, can't shoot or interact with him in anyway, yet when I go there my companions begin shooting at him as he is seen as hostile...so I can no longer use the red rocket as a home base.
I have Pallidan Danse at the castle. And I sided with the brother hood but let him live. So idk if that's my problem. But I can't talk to Danse because he won't stop firing