I collect potions up to 64 in my player inventory and chests. But if I have collected bottles and shift-click with brewing_stand window opened, all of 64 potions are placed in the stand. Even if I tried

inventory:
brewing_stand:
disabled: true

OR

inventory:
brewing_stand:
potion: 1

Try using "brewing" instead of "brewing_stand". I should probably document this somewhere if it isn't already. I believe I set this up to use Bukkit's inventory names, which can be confusing at times.