Brewing stand slots are set to only be allowed a single item per slot. To this end, shift clicking behavior is set to only attempt to place an item into the brewing stand if it's a valid item and if its stack size is 1, but if a glass bottle is in the stand already, and a shift click is attempted, it will stack the bottles in the brewing stand.

This is a symptom of the larger problem being that shift clicking code does not take into account the max stack size of a slot, nor its inventory's max stack size, but only considers the max stack size of an item itself. This seems to be the reason you can't shift click a stack of more than 1 inside a brewing stand UI, to prevent this bug from showing up. I assume this is the same reason shift clicking inside of beacons does not work for stacks that are more than 1. A more comprehensive solution to this problem would be fixing the shift clicking code to respect slot and inventory max stack sizes rather than focusing on brewing stands.