Placing items directly into a hopper causes the items to be pushed into the chest/hopper but doesn't remove them from the hopper creating duplicates.
Linked issues
Comments 7
I'm having this same issue (but backwards), Win10 beta edition v0.15.6.
Chest > Hopper > Clocked Dropper Chain > Chest
Items placed in the chest don't disappear from the chest, but you can hear the clocks start on the droppers. So, you can remove the item, walk to the other chest, and collect the duplicate.
This bug has been reported to our internal bug tracker for further testing and a fix. It is scheduled to be fixed in one of the future updates (no specific date can be provided).
When placing single items into the hopper, they now immediately move into the chest. I tried other way of selecting items in the hopper and chest and could not duplicate things. Seems fixed to me.
Confirmed; the hoppers' contents do not leave the hopper visually until you exit the hopper gui, meaning that you can add and remove a single item several times, AND it duplicates in the chest also.