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.
Duplicate of MC-6228, please use the search function to see if your bug has already been submitted. Currently over 45% of tickets are being closed as duplicate.