When a hopper is trying to output items to another block/minecart, it only tries to output its first stack. For example, if a hopper's first stack is diamonds, and its second stack is iron ingots, and it's trying to output items to a chest which has each 1 iron ingot in each of its slots, it will not output any iron ingots to that chest, because it only tries to output the diamond.
This was previously marked Resolved as Duplicate of another similar bug, but is actually a distinct bug that was not fixed in 12w04a.
Duplicate of MC-8193, please use the search function to see if your bug has already been submitted. Currently over 49% of tickets are being closed as duplicate.