If you have a chain of hoppers that are all deactivated at the same time, sometimes the items don't go into a container in the right order. Here's when I noticed the problem after taking forever trying to make a working giant crafter lol.
I'm making a giant working crafter and WHY are the hoppers not going in order?! : r/redstone (reddit.com)
MC-273874
Hoppers are inconsistent with item movement ticks
Resolved
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0
The reddit video linked is in a modded enviornment (REI is present).