When i first entered the Bone Keep through the sewers i gained some faction reputation for the principality and the scavengers, so far no problem.
Though after getting the necromancy stone, i decided to go back to the keep's courtyard because i did not fully explore it yet. I then used the 2nd and 3rd sewer entrances to see, if they would bring me to the same location inside the keep.
However, both times when I entered the keep again, I also gained more faction reputation. Therefore my reputation with those two factions is maxed out, even though I only did my 3rd quest for the council.