With the new mechanic of hotbar saving, items can be ignored by the button to clear the inventory.

Way to reproduce:

-fill completely a hotbar with differents items
-save this hotbar in a save slot
-middle click on a block to get a new item in a slot of your hotbar, the previous item will go in your inventory
-reload your saved hotbar, you now have your hotbar and a copy of one of its item in your inventory.
-clear your inventory, your hotbar is clear, but the item in your inventory will still be there.