If the /item command is used to replace a player's inventory, armor, or offhand slot with a new item, and the item is then quickly removed from that slot by clicking on the item, the slot will not update correctly. When a command or the nbt target selector argument is used to read data from that slot, the game still considers the slot to be occupied by the item that was removed. It remains in this state until being updated, such as by running a /clear command or by placing a new item in that slot.

(Haven't tested this with containers or other forms of item slots yet.)

Images show:

The /item command used.

The /clear command reportedly clearing an item from an empty inventory due to the bugged item slot.

The nbt target selector argument also reportedly locating an item in an empty inventory slot due to this bug.