When I put water bottles in a hopper above an empty brewing stand, it dosent fill up with them, but works fine with potion ingredients.
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"Works As Intended". A hopper has to be placed on the side of a brewing stand in order to push water bottles. See http://minecraft.gamepedia.com/Hopper
"Works As Intended". A hopper has to be placed on the side of a brewing stand in order to push water bottles. See http://minecraft.gamepedia.com/Hopper