Because I ended up with two... I followed the BoS up until it was time to power up the huge robot, but then decided to go with Minutemen after all. Now the Institute and the Railroad are wiped out, but BoS and Minutemen are still around. The minutemen call me general and the BoS tell me things like 'How about including your brothers next time you run an op' and such so they still see me as an ally. Also, i still can do the Preston garvey quests and the BoS apprentice quests.
Did I glitch it out or is this just one of the possible outcomes?