The /clear command does not work properly with command blocks

When used in a command block, /clear will output a signal if it successfully clears the player's inventory. If the player opens a chest and clicks on an item in the chest which a nearby command block is supposed to take from the player's inventory, the command block will think that the command was run successfully because it found a player with the item.
Because the player did not have the item in their inventory, but was in fact holding it in their hand, the command does not actually clear the item from their inventory. When the player clicks on a slot in their inventory to put the item in their inventory, the command block seems to have a 'cooldown'. It will not clear the item properly for a while, even if it is powered again.