Minecraft command destroy block scoreboard?

I have a few command blocks set up so that when i'm holding a certain item and break a certain thing, it destroys all of that thing in a 3x2x3 area… The problem is that it doesn't ONLY destroy that thing, it destroys EVERYTHING.
execute @p[score_PockyPickaxe_min=1] ~ ~ ~ fill ~-3 ~ ~-3 ~3 ~1 ~3 air 0 destroy stone
this command is supposed to destroy stone blocks only, but it doesn't work. I'm playing on the stable 1.9 release of minecraft, any solutions would be greatly appreciated.

First, type these commands:
/scoreboard objectives add CobbleMined stat.mineBlock.4
/scoreboard objectives setdisplay sidebar CobbleMined

This will track a single type of block mined; however, for multiple types of blocks, the size of the mechanism is probably about 7x(3N)x1. This means that for 2 types of blocks, you need a 7x6x1 space, and for 20 types of blocks, you would need about a 7x60x1 space. This is not an easy solution, but it can be done.

A similar method can be used to track blocks placed, but to use them at the same time is more complicated still. We would, however, be happy to provide you with more information if you would still like to continue with this complex and bulky mechanism.