When setting up a command block to clear a specific item from the inventory, ie. clear @p 276, instead of clearing just that item, it also clears any items held in the inventory (by this I mean having clicked on an item in your inventory and are moving it to a different spot in the inventory. Also if taking an item out of the creative list. This does not occur if inside of a chest, furnace, dispenser or other such inventories. It only occurs in creative mode, at the moment the command block receives the pulse, and to items other than the item i specified by the command block.
Duplicate of MC-18627, please use the search function to see if your bug has already been submitted. Currently over 58% of tickets are being closed as duplicate.