So, my battle of bunker hill was peculiar. Spoilers follow;
[So, I'm working with the Railroad, within the Institute, and I get the quest for Bunker Hill, so I warn the Railroad, but not the Brotherhood.
i turn up and meet the courser, and we head up to Bunker Hill, and just outside the gate drops down a BoS Vertibird, which drops off two Knights in armour, and goes flying around.
The courser and synths fight the BoS while the RR are inside taking potshots. The synths die, I take out the Vertibird, Courser kills a knight, a Legendary Mirelurk from nowhere kills the last one, and then I assassinate the courser, all outside the front gate.
There is still firing going on, and I assume from outside the other edges, as on my last pro-BoS playthrough the fight was much bigger and stretched around the town. However there are no synths/BoS outside, but the gunfire continues. I head inside and the Railroad guys are going mad, shooting everywhere. And then I see at what.
The settlers and caravaners, who are all essential for this.
There are heavies firing Guass Rifles at Brahmin, Trashcan Carla being mowed down (repeatedly). a Heavy unloading clip after clip into Megs, the little girl who gives you a 'tour', face.
I've no idea what is happening for the Railroad to be shooting civvies.
I head into the bunker where the escaped synths are, unsure of what I should be doing, and downstairs is a group of BoS Knights fighting the Railroad! Except, I can't target any of them.
They take no damage. VATS acts as if no one is there. They aren't targetting me (although hanrooster targets them). I take damage from their thrown grenades, and the Railroad turrets shoot at me and do damage, but I can't shoot back.
I leave, unsure that I was supposed to go down there if I wasn't with the BoS or Institute.
I travel to meet Father on the roof of CIT. I tell him it was an ambush.
He berates me though for the Brotherhood finding out about the secret mission, even though I didn't tell them!
I finish the mission thoroughly confused.]