Auto-crafting leads to items being destroyed

When crafting multiple of the same item, it is possible for the items required to craft that item to be destroyed.

Take the beacon (for example). If I have 2 stacks of glass, 2 stacks of obsidian, and a stack of nether stars in my inventory, I can craft 25 beacons.

If I want to craft more than 25 beacons, but the rest of my inventory is full, I may try to throw some glass/obsidian on the ground, so that I pick it up when some materials have already been moved into the crafting table.

I open the crafting table, and shift-click the beacon icon in the auto-crafting menu. Space in my inventory opens up, and I auto-pick up an extra stack of glass and a stack of obsidian (thrown on the ground previously) without exiting the table. I then shift-click the beacon icon again, to add this glass and obsidian into the crafting table (with the required extra nether stars). 

When this happens, the behind-the-scenes maths that works out how many of each item to put into each slot starts putting 38 of each item into the required space in the crafting table. However, it only uses the ORIGINAL values of glass/obsidian/nether stars, and the extra stack of glass and obsidian that I picked up from the ground are removed. They no longer exist.