Well crap. Last night, I got caught hacking into KL-E-0′s terminal, everyone attacked me, then I went back to Red Rocket to change my companion, and I walked into a hellfire of my companions attacking MacCready, then he started shooting at me. Is this a glitch in the AI that he’d even know about that? Will he ever STOP?

Looks like the Goodneighbor faction went hostile to the player faction to me.
MacCready is part of the Goodneighbor faction, btw.

I saw something similar with settlement defenses and companions firing on BoS vertibirds, but only happening in the settlement Danse was in.
In this case it was the presence of Danse in the Settlement.

Inter Faction AI is the culprit on this.