Well, it happened again, same enemy, same spot, that guy with the sword guarding the wheelchair gunman in the Derelict Building.
One thing I noticed is that sometimes he drops an item that you get a quick prompt for but it falls through the ground before you can nab it. It seems if you grab an item whose fate is to collide, it breaks your game. So this is definitely a specific bug with a specific enemy in a specific spot. (I am playing 1.04 btw, issue still here as it was in 1.03)