When setting a custom item in the result during the PrepareItemCraftEvent by calling event.getInventory().setResult(), then shift-clicking the custom item set, the amount of items produced is incorrect.

Example code:

@EventHandler
public void prepareItem(PrepareItemCraftEvent e) {
    e.getInventory().setResult(new ItemStack(Material.DIAMOND));
}

When placing, for example, a stack of Stone, and shift-clicking the Diamond produced, you receive 27 Diamonds instead of 64, but the whole stack of Stone is used.