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.