For now, only with female thug, just after second terminal (that one you can’t hack without upgrade). Never occurred (yet) with male thugs, but I never proceed past that section (have little time to play, plus because of this bug «pacifist run» constantly failing on this section, which kills my mood to play). Also, «move the body» prompt always works first, even if theres another enemy, so you can’t stun/kill two guys in a row, but I guess, theres just no optimal way to deal with that?
To me, it's random; some are registering, some aren't, sometimes even in a row. You can’t predict which ones will work.
Sorry for broken grammar.