In the kill command, it seems to be ignoring the Damage value in the json. for instance, I want to prevent the player from mining Andesite, so I want to kill the entity. They are allowed to mine other stones, but the andesite I want to prevent.

I setup a clock with a command block to detect when a stone entity is dropped, and fed it into a command block to kill only stone with damage value of 6.

kill @e[type=Item] {Item:{id:minecraft:stone,Damage:6s}}

It kills all stone, ignoring the damage value for polished andesite.