If I set potions to stack to 16 by default, even if I make an override for brewing stands to only stack 1, placing stacked potions by left or right-clicking in a brewing stand slot sometimes places the whole stack instead of just one.

I haven't been able to replicate this issue. If you're still experiencing it, please let me know and provide your current configuration and any steps you can to help replicate it.

I don't think I've changed my config settings for this plugin since the last time I was asked.
data/blastfurnaces.yml: default (blank)
data/furnaces.yml: default (blank)
data/smokers.yml: default (blank)
lists/customfuel.txt: default (blank)
furnaceXP.yml: default
groups.yml: default (blank)
items.yml: potions stack to 16 in the inventory or most containers, but to 1 in brewing stands so people can't make 48 potions from the same amount of ingredients one could use to make 3.
options.yml: default

As you can see from this gif recording, it is by no means consistent, and does not, at least to my knowledge, involve any previously recorded bugs.

If you need more information on my server, let me know.

I am starting to wonder if this is something server specific. Your gif looks like it might be the drag to place multiple action causing it, but I can't get it to happen on my end.

For testing purposes, can you replicate this by taking a stack of potions and dragging it within a single slot in order to drop it? For my ability to test this though, would you be able to zip up your server and send it to me so that I can test the exact setup you have?

You seem to be correct, dragging a stack of potions across a single slot, then releasing it, does cause the entire stack to enter the slot.

I am making a server backup now. It is on the order of several gigabytes, so it will take a while.

I am making a server backup now. It is on the order of several gigabytes, so it will take a while.

Feel free to exclude the worlds folders to help reduce file size

https://drive.google.com/file/d/13son2BE0wOXWZGm3HHZvsLI-5DZ_h_Tj/view?usp=sharing

Looks like it's private, but I've requested permission on it. Alternatively, you can make it public.

My apologies. I don't use Google Drive much.

Can you try changing your configuration from "brewing_stand" to "brewing":

    brewing_stand: #Override for brewing stand
      potion: 1
      splash_potion: 1
      lingering_potion: 1

to

    brewing: #Override for brewing stand
      potion: 1
      splash_potion: 1
      lingering_potion: 1

EDIT: Also, your "crafting_table" should be set as "workbench". I'm also adding a warning message on load for invalid inventories going forward, which should help prevent issues like this.

Alright, I'll check to see if that solves the issue.

That seems to have fixed it. Thanks!
I had thought that CRAFTING_TABLE and BREWING_STAND were valid inventory types, but after re-examining spigot's documentation, I can say for certain that they were not. I don't know where I got those from. Assuming, probably.

I think the confusion is that those are valid Material types, where this is looking for Inventory types, which of course are slightly different.