When I was playing with minecraft 1.10.2, there's no such bug, I'm sure it could be a bug, rather than a `feature'.
How to produce:
put a hopper on the ground next to a chest, put a brewing stand on the hopper, put another hopper next to it. Then put 5 bottles in the hopper which next to the brewing stand, then you can see the hopper which was under the brewing stand, sucked 3 bottles and inject them to the chest, but there's still 2 bottles in the hopper and could not be injected to the brewing stand.
Before 1.11.2, we created an automatic brewing machine, and it worked well. But after we updated the server to 1.11.2, the brewing machine could only brew 3 bottles of potions.
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Recreated this myself on a server last night. Hoppers will feed "through" the brewing stand until you lock them to actually brew something. The water bottle hopper will never unlock even after all Radstone is removed. The only way to unlock the hopper is to break the brewing stand and replace it. The hoppers will work as normal again until the bottom one is locked. The side hopper will then never unlock.
Duplicate of MC-111753. Please go and upvote that ticket instead. Also please use the search function next time before creating a ticket to save everyone a lot of time.