Hey guys, I've done a couple of google searches about this problem after i started having it happen to me, and found that a lot of people have had to deal with this. I don't know if this is really a "fix," but i saved and logged back into my game and the separate stacks have combined. i don't know if new potions will continue to not stack (i'm low on useful items right now), but it looks like you can just save, quit the game, and turn it back on, and it should fix the stacks if you're running out of space. also, my connection was really slow during most of the playthrough that had the potion bug, so maybe the bug has to do with steam lagging? just a thought.
This is a known bug that should (hopefully) be fixed in the upcoming update. I HAVE been able to fix the issue at least once by saving the game and reloading it, but I can't swear that this always works.
It's worked for me everytime. I think the bug goes like this: -You break a stack with a crafting tool, it won't be going into the stack again. -You craft a new potion, it won't go into the stack. -Newly crafted potions *do* stack on each other nicely, they just won't do so with your previous stack. -Potions parted from the stack with crafting tool won't stack with each other. AFAIK, it affects health, mana, and "reagent" potions, I think it doesn't affect empowerment potions. But I'm not sure... When I find that bug (quite often, it's annoying) I just put all the stacks in the inventory (leaving things in the ground... I just need to take everything that isn't nailed down), save'n'quit, load game, sort, and it's fix'd.