Minecraft command destroy block scoreboard?

hello, 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.

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