Currently I have two Cyberpsycho GIGs unfinished, despite win fight with mini bosses. I think problem is related to some clipping objects below the ground. I had this in other quests like those for NCPD. Sometimes you neutralize some of the enemies but go around location to not raise the alarm to finish others. So if I go back to this place again, bodies are hidden under ground and I have no way to get items on them. So if shard is in the box, then quest is finished. If is on the body, then you can't finish it if body sunk into the ground.
I hope that CDPR bring back the debug console, otherwise there is no way to get all quests properly done.
Debug console back would be easier to get, than fix all those bugs with object disappearance.