Assuming your stones are seperate sprites, the condition and action you just described should only destroy the stone that is clicked.
If you want to destroy the stone after touching it a certain number of times (eg Terraria with a weak pickaxe), you can add a local variable to each type of stone. For example, each "normal stone" could be worth 5.
Then you create condition:
Mouse click on stone = subtract 1 from local variable.
Local variable equal to 0 = destroy object
Again, as long as your stones are separate instances of the object, only the instance that is being clicked will be affected.