Using "pick block" on non-stackable items in the hopper's inventory sometimes creates ghost items.
Steps to reproduce:
Place a chest with a hopper above it.
Prepare a non-stackable item in your inventory.
Use "Use Item" (right-click) key on hopper to show the hopper's inventory.
Use "Pick Block" (middle-click) key to pick the non-stackable item.
Place the item on the hopper's inventory and immediately use "Pick Block" to pick the placed item.
(Optional) Repeat the above step (#6).
Sometimes the picked item using "Pick Block" will be a ghost item. You can still place it in the hopper and continue using "Pick Block" on it, but it wouldn't be "hopped" into the chest below and will disappear upon leaving the inventory screen. When you attempt to use it or left-click on it, all the related ghost items will immediately disappear without doing anything.
Tested items:
All types of Minecarts
Boat
Splash Potion of Weakness
Diamond Sword
Related issues
duplicates
Comments

Resolving all "Pick Block creates infinite/ghost items" to one ticket.