The potions can not enter the brewing stands through hoppers

You need a hopper and a brewing stand, some blaze powder and some ingredients.
Try putting the water bottles into the brewing stand throught the hopper.

If you are using another hopper to clear the brewing stand from the crafted potions, and you try unsing another hopper to fill the brewing stand again, here the bug happens.
Probably the brewing stand isn't properly cleared when the crafted potions are absorbed by a hopper

If you reload the map, the options are going into the brewing stand, but you need to reload the map for each potion you want to transmit

i tried it in solo and on a spigot server, in the two cases, the bug happened

Sorry for my really bad english.