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.