why is it that sometimes if i break a block, it dose not dissapere but it harms my tool?

This is caused by lag/low tickrate - you break the block quickly, but the (potentially integrated) server thinks time is slower so it doesn't think you broke it all the way and thus rejects the break. (I'm pretty sure MC-858 is the right issue for this, but there might be a different one)

It's worth noting that your tool isn't actually damaged - if you right-click with it afterwards (or move the item in your inventory, or relog) then the durability will reset.