The following can occur in any case where a crafting output yields more than one item. For this description, I'll use cobblestone slabs.

1. Fill up all but one inventory slot. This should include three stacks of cobblestone.

2. Open a crafting table, and place the three stacks of cobblestone in a horizontal line (i.e. craft cobblestone slabs). Shift-click on the slabs which appear in the "output" box.

Since you had one free inventory slot initially, and you used three stacks of cobblestone for crafting, you have four inventory slots open. All four of these slots will fill with full stacks of cobblestone slabs.

3. Dump some items to give yourself some free inventory space, then craft the rest of the cobblestone into slabs.

As a result of the bug, you will now have 5 stacks + 62 cobblestone slabs. Since cobblestone is crafted into slabs in a 1:2 ratio, this is two slabs short of the correct amount.

This bug occurs because when players shift-click, the game attempts to give them as much of the output as possible. At some point, the player's inventory is completely full, but one inventory space is occupied by 60 slabs. The game notes that the player has room for 4 more slabs, and so three cobblestone items are removed from the crafting grid. Since slabs can only be crafted in batches of 6, however, the player is given as many as he can hold (4 slabs) and the remaining two are deleted.

This would best be resolved by slightly modifying the shift-click mechanics; rather than constantly trying to fill the player's inventory, the game should make sure that the player can hold all of the crafted items.