I have several caves, tombs, etc. that I have visited and finished. However, when I scroll over these places on my map it does not say "Cleared" next to it. Also, I have gone back to these places and gone through them thoroughly and can't seem to find any rooms I have missed. For the most part, every place I go to and finish says "Cleared" except for a few. Does that mean I missed something in there or is this a bug? Thank in advance.

they might be part of a quest that will unlock a hidden room that is not in plain sight.