Potions can't be pushed into brewing stands via hoppers.

Hoppers won't push potions (or water bottles) into the brewing stand(regardless of existing contents). The only way to do so is to manually remove the bottles already in the stand. Even pulling them out with a hopper underneath the stand won't allow the new potions to come in. The only way it sometimes works is if the feeding hopper and the brewing stand are empty and bottles are shift clicked into the hopper.