This can be resolved as fixed. 1.6.1

When using the /clear command for specific item(s) or a specific amount of items, the chat message displays that the full number of items in the player's inventory has been cleared, despite many fewer items having actually been cleared.

For example;
1) Say you have an inventory full of Baked Potatoes. (2304 potatoes (why do you need so many? the world may never know...))

2) A command is executed that is meant to clear out only 64 Baked Potatoes.

3) The command goes through and the following incorrect message is displayed. (The message claims that 2304 items have been cleared, despite the command only removing 64 Baked Potatoes)

4) And by checking the inventory, we can see that in fact only 64 Baked Potatoes were removed.