This happened to me a few times when an enemy got suppressed in a small room or container and the door closed before they came back out or came out for the first time. Eventually I pulsed or used a seeker mine to find them and from my personal experience you can sometimes get lucky and see a hand or foot or something of them and be able to shoot that small piece of them to kill them. Sometimes but not all the time. I’ve seen this happen or have been able to do this with targets in cover like if some of their body flashes through a wall or barrier.
Not a perfect fix but can work at times.