Any enemy that has the 'Doesn't Count AS Beatable Enemy' flag checked can be killed by the death of the ring leader or the kill all enemies item. In versions prior to 1104, enemies with the 'Is Invincible' flag checked, such as traps, could not be killed by the ring leader's death or the kill all enemies item, with the exception of Phantom Ghinis, but now they can be killed by such even if they are invincible and don't count as beatable enemies, with the exception of projectile shooters. Things like traps and rocks were never intended to be killed by such, neither were the bubbles (which are normally invincible) in the default template!
The point is invincible enemies with the 'Doesn't Count As Beatable Enemy' flag checked are kill-able by the ring leader's death and the kill all enemies item when they shouldn't be!