When making changes to large amounts of items, like changing bones to bonemeal, once the inventory gets full items should start getting thrown on the ground. If you continue to click rapidly to finish converting the bones to bonemeal the bonemeal item still get stuck on your cursor and you will be unable to throw it down. If you try to craft more of this item you will see the bones try to convert, their number will change to a lower quantity and then go back to their original quantity. 

Closing and reopening your inventory does not fix the issue. The only way I have been able to fix the issue is to log off and back on. When you log off and back on and open your inventory you will still be holding the stack of converted items and be able to throw them on the ground. I included a screenshot doing the same thing but converting large quantities of iron blocks to bars.