I have noticed the following:
I have killed every last bandit (or mage or whatever) from some forts and the map won't read "cleared." So I continue to look around thinking I must have missed a room or something somewhere and then, still finding nothing, just move. Later, that fort turns up occupied by Stormcloak or Legion even though the map never indicated "cleared."
On other occasions, I have gotten the "cleared" tag on the map and then on a subsequent trip by/through that fort, I get bandits shooting at me even though the map still reads "cleared".
Anybody notice anything similar?

They will usually respawn in three days, so if you've been off on the other side of the world for a bit, that would explain why there's more bandits when you go back.

i think the *cleared is to more be used as a ''oh ok ive done that already'' but after 30days enimies respawn or it can be a new type of enemy there, once everything is dead it doesnt stay dead its not a linear game things respawn and move in all the time.

also if the place is part of a quest for later maybe the clear* tag wont show on some things.

Also, not all the dungeons get marked as "cleared" for whatever reason...

Dungeons are marked Cleared when you kill the Dungeon Boss. I have read somewhere that you may have to also loot the Boss chest to get the Cleared, but I don't think that is true. Not all dungeons have bosses at all times in the game. Bandit Chief is not always the boss, that is just an NPC type, like Forsworn Pillager.

So, it could be that there was no boss at the locations you have cleared as the game has not put one there yet. Plus, all dungeons respawn after a period of time. Don't know if it is 73 hours or 31 days or some number in between.

The other weird thing is the game can put a boss in a dungeon for a Radiant Quest that already has a boss, so you get two of them.

Love Skyrim's forts, absolutely worthless for defense.

Some of the bandit occupied forts don't show as cleared because in the Civil War questline thei're meant to be occupied by one side or the other and play a role in some quests.

Probably half of the reason for that is because up until they meet you, no one else in the world knows how to jump.

According to the Prima guide, Forts Dunstad, Kastav, Greenwall, and Amol are taken over by either the Imperials or Stormcloaks during the Civil War questline, so clearings of bandits, mages or other scum wont mark those forts as cleared.