I don't have such problems (enemies from the sky), but I have another.
I clear location (fully, I know there is no enemies anymore), make fast travel, return back- and see enemies again. Not in the same number, only a few, but of the same type. May be it is some type of the overflow for the engine in placing so much actors
Have similar issue, I just have to change cell example go inside a building then straight out again and there are enemies has respawned, wait an hour and they pop out or save/load a game.
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