So I completed the game with the Institute, destroyed the Brotherhood blimp and everything, and killed everyone in the Railroad. I've been playing the game for like 50 hours since then, and every so often the Institute asks me to help them with their checkpoints. I also go and do it, and it's always either gunners, raiders or ghouls. However, recently it was the Brotherhood! We killed them all but I was a little surprised that they were even there at all. The next time it was Railroad agents. So I went to the Cambridge police station, and started getting shot at by Brotherhood guys. I killed them all and then went to Railroad HQ, but there was no one there. Am I missing something? Any answers would be appreciated.
Some of the high placed individuals from whatever faction you side with, will tell you that you may have beaten the enemy, but that still pockets of troops remain. They state that the purpose of the missions where are tasked to remove those enemies from a checkpoint are to ensure the ememy does not reorganize itself and starts posing a threat again.
This would make sense, since the brotherhood may have had people send out on missions, railroad operatives could be hiding, and so on. And after learning that their HQ was destroyed, they might form some sort of resistance movement (again)(this won't happen in the game, but it's their way of justifing these radiant quests).
So this is supposed to happen. As for the Boston police station, perhaps after you have cleared it out the first time, no more Brotherhood soldiers will spawn, but instead gunners or raiders.