The hell is going on here? I'm sided with the Minutemen, I destroyed the Institute, never had anything to do with the Railroad beside making them crack the Courser chip, I just went to Bunker Hill to find where the hell Trashcan Carla was supposed to be and everyone is shooting at me. Moreover, the synths fighting there are friendly. WTF?

You probably did not gave the evacuation signal when you destroyed the institute.

Nope, did that.

I think there's something wrong with bunker hill, or the quest related... After doing that (and I suppose you do) it becomes a normal settlement, just like any other.

There are no railroads there... Have you try going in Railroad HQ?

You "failed" the battle of bunker hill which causes a bug where the battle is never resolved and goes on forever. Why the Railroad is shooting at you I don't know, the fact you never had any contact with them aside from cracking the chip could be a part of it.

I had to go back and wait tell Mass Fusion to betray the Institute to prevent that bug.