Do all dungeons, caves, etc eventually give you a cleared message? There are a few that I have gone all the way through to the end (or at least thought I did) and did not get the cleared message. Most of the time after I leave a location it will tell me cleared though. However, I noticed that I had a quest in the bandit's den or whatever it's called, finished that and then later got another quest that took me back there. Still don't have cleared on that location, so I wondered if it was due to there being more quests later for that location?

The objectives for clearing a dungeo is usually taking end loot or destroying the boss. Going out the backdoor can often result in that too.

Usually killing the boss in a cave clears it for me. Did chilling and suspected I hadn't gotten everything and no clear message and found that I was missing the corridor that led to the boss chamber and quick exit. If you don't fight someone tough, you haven't cleared it.