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.