I've seen it before, albeit in a very complicated setup that was difficult to reproduce and highly visible. Are all the mechanisms making it indestructable also impossible to damage from outside the bunker?
My guess is minecarts, boats, small animals (chickens?) or some such tiny entity. Whatever it is, the hitbox is protruding past the block - but the entity itself isn't. So, you can only hit it in a very specific spot (where the hitbox does not protrude).