Generally after I finish a dungeon, dwarven ruin, etc. (with the exception of forts) a small cleared appears below the name. However some of the areas that I have cleared aren't showing as cleared. I have checked and most of these locations don't have any quests associated with them. I try to use this to keep track of the areas (as best I can) that I have already explored. Does this happen to other people. or is there something else that I need to do so that they show up as cleared. Thanks for any help.

Yea I've got a few that don't clear, though most do have a quest for them. Check out the locations on the UESP. Each location's page tells if it clears or not.