In Skyrim there are several forts occupied by bandits, necromancers or Forsworn.

When the civil war questline is started, some of these forts are magically 'cleaned' of their former inhabitants and a faction hostile to the player is spawned until the quest of capturing a given fort is completed.

I would like to discuss what happens to these forts outside the civil war and why the 'cleared' label is given to them.

Fort Neugrad, near Helgen, is full of bandits. Once you clear it, it will be inhabited by soldiers: note that the "cleared" flag is never set no.

This seems to be an exception: other forts such as Sungard, Greenwall, Snowhawk, etc will be populated again by bandits or necromancer when cleared outside of the main quest. Again no "cleared" flag is set.

So,

1) what's necessary to do to have them cleared?
2) why only one fort seems tp be repopulated by soldiers once it's cleared for the first time?

You have to defeat the 'boss' inside the dungeon to have them cleared.

However, based on my own experience, some dungeons don't clear, like the wolf queen cave near Solitude. And some 'cleared' dungeons respawn enemies inside, what's worse is that NPC's radiant quests point you back to them.

I stopped caring about the 'cleared' thing after I found out the above.

I know. It's not even necessary to defeat all the lesser enemies. After said 'boss' is defeated a sound should play signaling that the objective has been reached.

What I'm asking is why all the forts but one are again repopulated by random bandits and not claimed back by the military forces present in that region. This and the lack or a 'cleared' tag makes me think that this aspect of Skyrim is either bugged or was rushed.

actually once you clear most of them, outside of the civil war questline, they do get taken over by the military.

there are some however that you don't seem to be able to clear.