Fallout 4 brotherhood and railroad returning after game completion with Institute

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.