When I go through most / many locations, after all the bad guys are gone, it shows " cleared " on the map.

But not all of them.

Which makes me wonder if I " got " all the bad guys or not.

Should EVERY location show " cleared " on the map after you clear out the bad guys?

I wish there was a mod that showed how many bad guys were left in a location.

Areas do respawn, does the 'cleared' flag disappear when somebody else moves in?

it depends, some areas stay "cleared" others get cleared and respawn, having the "cleared" message disappear, and yet others don't ever seem to get cleared (or I missed something anyway) and some are respawned even when it says cleared. Basically, "cleared" should be taken with a grain of salt til you know how the area works.

Seems it's a bit buggy, I had Corvega respawn 3 times before the Cleared message disappeared on the 4th. Excellent place to score some Aluminium