Why did some of them survive?
Why did the mobs keep spawning even when you turned the lever off?
Why did it go out of control?
Some of them "survived" because they didn't spawn right. Not sure how how or why it happens, but they bug out and appear in the wrong places etc. After running it I can find lots of them down in solid ground below the spawner... They are immune to all damage(including fall damage) and cannot be affected in any way. So assume something is going wrong in the spawning process.
It is the bees that reanimates them. That particular bee has a trait that causes any drop from Skeletons, Zombies or Blazes to disappear and spawn an equivalent mob instead. The lever was actually turning off the MFR grinders. I turned the Lever OFF to turn the grinders ON when the skeletons started multiplying, but they could not keep up at that point
It goes out of control because each skeleton drops a bone and several arrows. Both the bone and the arrows count as an item that can be Reanimated by the bee. Therefore it escalates out of control VERY quickly
Zombies will not go out of control in the same way, but they were also not sustainable as they didn't always drop an item.
In the picture I posted I took control of the drops by adding them through a Dropper and feeding them into range with Conveyors. So no more running out of control