The only reason it should be doing that is if you're waiting too long to get the nuke dropped and then putting it in. The wipe wave that the boss spawns is most likely hitting you right as you're putting it in. I'd recommend just instantly killing the enemy that holds the nuke as soon as it spawns and then just leaving it on the ground until the boss goes immune. The nuke has more than enough time to sit on the ground until the boss goes immune and sends the wipe wave. That way, you only have to grab the nuke and run to the room instead of killing the enemy holding it right when the boss goes immune.