When shift-clicking to craft a stack of bones into bone meal, when only one or two spaces are available in the inventory, the game produces full stacks of bone meal where multiples of three items should be created. This process means the final crafted item is fully consumed but only produces 1 or 2 items instead of its intended 3.

The same thing happens with other items. When a stack of blaze rods are taken, and shift-crafted into an inventory where all spaces are occupied, but one of them contains a single Blaze Powder item, then 32 blaze rods are consumed, but only 63 Blaze Powder item are added to the inventory, filling the stack to 64.

In this case, that final item should simply NOT be converted at all.

The screenshots show one bone meal item lost when shift-click crafting into an inventory where only two spaces are open.