I was walking around a pier kind of area, sorry not sure where exactly, there were synths around that I was taking out and out of nowhere a vertibird started firing on me.. No clue why.. So I chose not to kill it but run away so that the BoS wouldn't see me as an enemy but hours later in the game I ran into some BoS members fighting w super mutants who fired at me on sight. I don't understand what happened here, any ideas?? I haven't made any real faction choices and am not very far along in the main questline.

Did you ever go to the Police Station and help Danse before the BoS arrived?

It has happened to me, as well. To answer LeBurns' question, it was after I'd rescued Danse and and his sad-sack crew at the Cambridge Police Station.

From what I understand, sometimes raiders/gunners commandeer Vertibirds and it is THEY who are shooting at you. Whenever I see Birds in the air now, I try to see who is at the controls. Additionally, if BoS is fighting in an area, I usually try to stay out of it until they leave. I don't like BoS (hehe could you tell?), but I won't deliberately pick a fight with them. That said, if they engage me in a tussle, they WILL lose. Even the ones galumping about in the tin cans .

^ Yes, I've had a Vertibird with Gunners attacking twice.

Please note that you can safely shoot down Vertibirds without becoming hostile to the BoS. In my first play through I must of shot down at least a dozen of them, I stopped once I realized it was a waste of ammo as they have such awful pilots that they always crash on their own anyway.

You do have to be careful if you get into the middle of a fire fight with BoS ground forces, it is like defending a settlement, accidentally shoot a 'good guy' and they all become hostile.