I have discovered a redstone interaction bug in 1.11.2 that i found is also present in 1.11.1 where the brewing stand only accepts bottles from a hopper once if they then get removed by a hopper. This bug is non present in 1.10.2 and also doesnt happen anywhere when the player removes the bottles / potions from the brewing stand by himself.
To reproduce the problem :
A hopper feeds water bottles into a brewing stand from its side, under the brewing stand there is a hopper with a block underneath, under that block a torch to control the hopper, at the beggining the brewing stand fills up with water bottles, then when the hopper underneath is no longer powered, the bottles or potions do get pulled away, but then the brewing stand doesnt refill, until the world is reopened or water bottles are added in the brewing stand by the player.
The world in attachement contains the test i have made to figure that much of the problem.