When you go /clear @p stone 0 64 this should remove 64 items of stone if the player has 64, but it just still clears you if you have 1 item.
Another bug is that when you go "/? clear" it only says "/clear <player> [item] [data]" when it should go "/clear <player> [item] [data] [Count]" so you know that the last number mean how many you clear.