Once a brewing stand has been placed, a hopper can refill the stand no problem. Once a hopper has extracted potions, the hoppers that refill the stand with water bottles do not refill the brewing stand. This happens when hoppers are facing down, North, East, West, and South. In order for the stand to be refilled with water bottles, the brewing stand must be broken, replaced, or refreshed.

The only time a bottle would replace a potion is if it were to be removed by a player, in which case the bottle would only refill the slot that was occupied by a potion. Then in that case, only 1 bottle will be taken from a hopper, thus this is not a visual bug.

Re-logging/refreshing the single player world would refresh the brewing stand, and allow a bottle to be put into the system, but just breaks again once extracted. Maybe a variable was not reset when automatically extracting a potion.

Picture 1: Setup of the test; new brewing stand with 3 potions in the inventory

Picture 2: Proof of all (one of the) the hoppers filled with water bottles to refill the brewing stand

Picture 3: Removing the redstone signal from the hopper to extract the 3 bottles currently inside. The brewing stand does not fill back up with bottles

Picture 4: Showing that the 3 water bottles have been extracted, no more, no less. (The extra one in my inventory was a test to see if putting one manually in the brewing would be extracted, it did)

Edit: Has not been tested in multiplayer as of yet