We found a way to deal with it and also noticed when it happens.
Our group make up was Assassin, Sorc, Jugg and BH.
When it scanned any of them except me (BH) we were fine with one clone. The second I was scanned the fight would go nuts and a ton of NPC would be scanned. The multiples would not be always mercs they were all random.
What we did was click on the panel behind the boss in the next room and we spawned directly behind the boss (Be prepared though as there are mobs in the room when you re-enter the room after you respawn.
We focused on the boss, killed one copy, went back to the boss and DPS/healed through to kill the boss. I would say the only part is luck is if the BH gets scanned last. As it gives you enough time to kill the boss. After the boss is dead ....the clones still keep respawning, no matter what so you will just have to die but at least you killed the boss.
We did find that it's was myself (bounty hunter class) that was causing the bug with him for sure. None of the other class made this bug out on the fight but from what I hear as well, that it happens with Operatives as well. Just a heads up and a way to get by that boss till they fix it as it's not "Working as intended" It's an obvious bug.