Only effects Creative mode.
Only effects item "held" by your cursor in inventory GUIs.
Edit: Upon further testing, this bug ceased to exist after rebooting the game.

To replicate this bug, put down a command block with the command "/clear [username] [any valid item ID]".

Hook a redstone clock to the command block, and open your inventory. Click on any item, and it gets deleted, even though it is not the item the command is supposed to clear.