Is there any rhyme or reason to it? I've yet to see a DEFINITIVE answer. I gather the popular thought has to do with either killing all the enemies/looting the 'master' (for lack of a better term) chest at the end of most dungeons, but I still swear it's not clearing a decent chunk of them for me.
Also I've heard that you can't clear dungeons that have quests involved until you do the quests, but I've cleared a dungeon (Broken Oar Grotto) and then done the quest (Lights Out!) afterwards so that seems to disprove that theory.
I just did the quest involving Wolfskull Cave and went throughout the dungeon, no clear.
I've gone through Brinewater Grotto, too, for example, and all that was there were those walrus-typed things and literally 1 room so I killed them and left. All enemies dead. No clear.
Shadowgreen cavern, just a big cave-forest thing that I walked around and fought a Cave Bear and a couple of Spriggans, went everywhere according to the map. All enemies dead. No clear.
Some of the forts haven't cleared for me, either. But the only ones that haven't for me are ones where some other group takes over later. Fort Amol, for example was taken over by Stormcloaks after you kill all the mages (that had apparently killed a bunch of Stormcloaks in the first place) So those seem to have an explanation at least.
I don't really want to chalk it up to me overlooking something because I'm usually very thorough when going through dungeons (a little perfectionist, which is why this whole no-clearing thing is annoying me so much in the first place). But I'll admit it's possible especially considering I don't know what constitutes a -clear-.
Sorry for the super-long post, appreciate any help that may come.
I can't say for the others but as far as brinewater goes here is the deal:
There is a thieves guild quest in which you are required to tail a man into some cave that start near solitude (starts in some trading company). At the end of this tunnel system where you finally meet the person you tailed there are several levers, one of these opens a hidden wall that exits into brinewater cavern. You cannot get a clear without opening this door.
Hope that helps, sorry for the generalizations but tried to avoid giving spoilers.