SPOILERS AHEAD

I completed the main story line about 60 hrs ago and I found out that what ever option you choose you will become hostile to 2 of the other factions....I wanted to destroy the institute with the BOS, but I accidentally ended up doing it with the minute men.

I destroyed the institute, but the Minute men, BOS, and Railroad are still allied to me. I even complete some of PAM's missions in which you go around killing the BOS and they don't seem to mind at all. I saw that in theory I am suppose to get the option for the mission Rockets Red Glare in order to blow up the BOS ship, but I haven't and I don't think I ever will :[.

Have any of y'all had this problem and if so how did you fix it? I'm on the Xbox One btw.

Also just completed the killshot perk with MacCready and got the OP 95% headshot all the time perk with it!