The hopper will only take items out of the container it is directly attached to, making it useless when trying to use it with large chests, requiring a second hopper to drain into the first one. It should recognize the large chest as one container. It also can't pull items out of a large chest, although there's a way around this using a second hopper. No such option exists with to pull items out of a storage minecart and into a large chest however, making this bug very frustrating.