Hoppers (with available space) are frequently ignoring items that are flowing over them in water streams. Items can even pass between a hopper and a top slab, which seems inconsistent with hopper behavior (accepting items less than a block above them).

EDIT: Further testing has shown the height of the item is not the problem, when aligned between blocks and slid over both hoppers and ice the items are still only being picked up a little more than half the time. It appears to only occur when the hopper contains items (not full, just 1-3 items in one slot and 4 empty slots).

EDIT#2: When the hopper was pointed to the side and a hopper below it was locked until the top hopper had enough items to put out a signal strength of 2 (simple sorter design), the top hopper only failed to pick up items when the signal strength was 2, it seems that hoppers sometimes ignore items they should pick up when items are are being removed from their inventory at the same time. Tested again with a hopper pointing into nothing and the behavior still occurred.

EDIT#3: Hoppers (with plenty of space) are not always able to pick up items if they recently picked up an item.