When setting up a chain of hoppers (fed by a single hopper which items go into via water stream), with a row of hoppers all going in a line and then 2 subsequent rows with the hoppers going into chests, a hopper which should not be getting items (as it's further along in the chain and the previous hoppers and chests have not filled up) steal items. 

The weirdest part is that only the hopper in the top row, next to the column that the items should be going down, and then the final hopper in the next column are showing the stolen items as well as the chest that the items are deposited in. 

I've tried many different configurations and what seems to be happening is a glitch where an item goes across to the next hopper in the top row instead of down, then skips all the hoppers between it and the last hopper in the next column to go there immediately.  Upon further testing, a workaround was found by having the first hopper in the chain (the one fed by the water stream) go down into the chain instead of horizontally into it.  However, this only reduces the items stolen from 10-15 to 1-2.

Hopefully, this is enough info to work off of.

P.S. I've linked a world download where I have a stripped-down version of the original setup.