This happened to me frequently when crafting redstone for auctions. I'd start with blocks and end up a dust or two short. I've finally tracked this down using iron blocks. If your inventory is full, crafting may result in some items vanishing into the void. Here are the steps (I've done this three times) a) Fill your inventory with stacks of something, like cobble. b) Leave 6 slots open. c) Grab a stack of 64 iron blocks. d) Open inventory, then "speed craft" the iron blocks into ingots. (shift-click the ingot crafting) e) Observe that 6 stacks of 64 ingots are crafted and 21 blocks remain. 64-blocks = 576 ingots. 21-blocks + 6x64 = 573 ingots. I am losing 3 ingots each time this happens. It looks like my inventory fills with as much iron as I can hold and the remainder of the division of an iron block is swallowed by the void.
I got some good news, and I got some bad news... The good news is that you're fully right, nicely observed. I tried to reproduce the problem and for sure. Note that you don't have to fill your inventory with stacks of stuff. Just filling it with cobble blocks and then leave the rest stacked will also do. So: At first everything looks normal, the excess which didn't fit in my inventory gets dropped on the ground. When picking it up it becomes a bit more obvious: And just to spell the whole thing out, this is what I ended up with: The bad news however is that this isn't something related to EMC. I fired up my redstone creations world (single player) and.... The exact same thing happened to me. So this isn't so much an EMC bug but a Minecraft bug.
A similar thing happens with the item drop flags. if you have a full inventory and you have an item in the crafting menu, when you close the crafting menu that item glitches out of existance.
