Hoppers will send items to a hopper directly bellow them instead of sending them to the container the hopper is pointed/aimed at.
Most prominent in the following configuration:http://i.imgur.com/AmAyZLO.png
MC-75824
Hopper Priority Glitch
Resolved
Invalid
0
it's not the upper hopper sending items to the lower hopper, but the lower hopper sucking the items out of the upper hopper.
You need to block the lower hopper by redstone to prevent that.