1. If I had one item like a axe in my inventory it might multiply and take up space in my inventory
2. If I open a furnace a chest or a crafting table and any other items that open up. When I close it, it will change my hotbar with other things in my inventory.
i have this same issue. Also and seemingly related, inventory items go missing regularly, and it seems to be when this issue of the working toolbar filling up with one item as you go in or out of chests.