The bug involves shift-clicking interactions with the Disk Drive. Shift-clicking an item out of the drive, and shift-clicking another item, will create a sort of 'ghost' version of the first item. The 'ghost' item will disappear when trying to stack or when held when attempting a right-click operation (whether it opening a GUI, or placing a block). The 'ghost' item will interact normally with GUI of blocks, and can be transmuted, macerated, store energy, burned, used in crafting recipes, etc.
A solution would be to disable the ComputerCraft Disk Drive.