Automatic brewing stand was one of my very first redstone projects in Minecraft.. It used to work fine since I started MC 1.8 before 1.11 came out..
I can 100% confirm that bug. The collection hopper (bottom one) works fine when putting bottles MANUALLY IN to the brewing stand. The feeding hopper (side one) works fine when putting bottles MANUALLY OUT from the brewing stand. They NEVER** work simultaneously.
**they accept only 3 bottles in/out when I teleport far away from them and back.
Confirmed in 17w15a... :'(