This has happened a few times to me -- I'll be traveling with a companion (most recently, Nick Valentine). I'll approach a defended location, and a BOS vertibird will appear. Next thing I know, my companion is chasing down that vertibird with murder on his mind. I figure (though I have no way to know for sure) that the companion was hit by some stray bullet (those miniguns send bullets flying in every different direction, even hitting the intended target once in a while). Once or twice, I've had a companion actually shoot down that vertibird. It doesn't seem to affect my relationship with the BOS, though -- they still don't fire on me if I don't fire on them.

OK, fine. Except that I am currently doing the quest at ARcjet systems with Paladin Danse (nick is still my 'official' companion, though). I exit the facility, start rooting around the area for junk as Danse yells something about not being alone (I hear a vertibird). When I'm done, I notice that Danse is now firing on a Vertibird! I do spot a Gunner somewhere around, but it seems like he's not the focus of the fight, that Danse and the VErtibird are locked in a death match. Nick was tagging along with me, so thankfully he's not involved directly.

Anyway, you may want to do something to make 'friendly fire' not trigger intra-factional combat at the very least. Having a way to put a leash on your follower (even followers other than Dogmeat) would not be sufficient, since once they start fighting, they tend to run all over the place. And besides, I tend to get hit by that minigun as well (I know I'm not the intended target because if I move away, I no longer get hit, though I have had a vertibird hover over me for no apparent reason, not actually firing, but maybe checking to see if I'm a hostile (?).

/edit Danse DID manage to shoot down the Vertibird. Also, I didn't realize it, but behind a tree was a caravan merchant who apparently also participated in the combat -- I don't know offhand what her part was in it, since I only spotted her after the Vertibird went down.

Also, Danse did not fire on the Gunner until after the Vertibird crashed -- I'm guessing that maybe the gunner should have been his top priority, and not the BOS Vertibird lol.

I had this happen too, except it was Piper and some rando Wastelanders suddenly firing on the Vertibird. Same situation: no prior conflict with the BoS.

I reloaded, and it happened again, so I used VATS to get a target lock on the Vertibird's occupants, and it turned out that a Gunner was piloting the Vertibird.


So, Gunners can steal Vertibirds apparently. That's also how I learned how easy it is to shoot one down.

To be fair, a much later situation elsewhere resulted in a firefight between some unrelated settlers and actual confirmed BoS, so that must have been a stray bullet or something because when I reloaded it didn't happen again.

Addendum: the Weston Water Treatment Plant west of Oberland Station is where I've most often seen the Gunner-piloted Vertibird.