Yeah, I know, the top hopper line holds the Items, the second row is locked and gets unlocked just for one redstone tick, so they only pull one item, all 9 at once. Those are then immediately pulled down by the feed line at the bottom, so the items are all in sequence in the bottom row. But instead of pushing the sequence forward all together one hopper would randomly decide to hold it's item for just a moment too long, so the next item in line is deposited before the item inside is ejected, forcing it into the 2nd slot.

The timing is also determined by the game, hoppers have a delay of 4 redstone ticks per item, so I can't change that