I can't be the only one who's annoyed when a place doesn't get the cleared tag even though you've killed every enemy you've found. Here is a list of places I have tried but couldn't clear. Add your own places and see if there are certain areas unable to be cleared.
Mass fusion containment shed
Mystic Pines
Lexington
Lexington apartments
Old gullet sinkhole
Skylanes flight 1981
Wildwood cemetary
Rotten landfill
Concord
Museum of freedom
Cave
Capsized factory
Hopesmarch pentcostal
Vertibird wreakage
Skylanes flight 1665
O'neil family manufacturing
Rocky cave
Decrepit factory
Crator of atom
Decayed reactor site
Atlantic offices
Federal Supply cache 84NE
South Boston high school
Waypoint echo
Edge of the glowing sea