Here is the situation in the attached screenshots. This hopper sits as the bottom of a mob farm, and is not currently connected to a chest. The second screenshot shows the inventory inside the hopper; there is Zombie Flesh, Gunpowder, Arrows, Bones, and Gold Nuggets.
The expected behavior would be that new items of these types would go into the hopper (until those slots were full) and other types of items would stay on top of the hopper. This works until the first item not already in the hopper lands on top. It does not go in (as expected) but all subsequent items stay on top as well, even though there is room for them inside. The hopper is 'clogged' by the unexpected item; this is illustrated in the first screenshot, showing Arrows, Bones, Gunpowder, and Eggs sitting on top of the hopper. Once the eggs landed on the hopper, no other items would enter, until the eggs were cleared.
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I'm having difficulty reproducing the behavior myself, actually. I originally saw the issue in a backup of an existing world, where I was testing hoppers with a mob system I previously built. I see the issue there, but not on the simple test I built blocks away, consisting of just a water stream and a hopper. Plenty of item duplication and invisible items bugs to be seen, but not the 'clogging' I reported. The hopper under the mob system (pictured) still shows the behavior, though. Every time and egg comes by, it completely clogs the hopper, and nothing can get through.
Can't reproduce in 13w01b.