I have gone through at least 4 monster brewer designs since 1.11 because of the brewstand bug. Then the weird one bottle thing started after that haha. I figured out it had to due with the timing and locking and unlocking the hopper feeding the stand. After dozens of redstone experiments on my test world and many hours of videos i found one that had a separate timer for the bottle release that worked from a fella named RabidSmore.

I made a few upgrades to the delivery, storage, and bottle filling station to make it nicer to look at and easier to use.