The brewing stand usually only lets you put one bottle in each potion slot, whether empty or filled. But if you have a stack of empty bottles, and you shift-click that stack into the stand, they all go into the same slot. So:

What I expected to happen: The empty bottles stack, when I shift click them into the brewing stand, should put one empty bottle in each slot.

What happened: The stack of empty bottles, instead of putting one in each slot, all went into one slot. Pictures below.