I don't know if this was an issue to begin with, but now alchemical items sometimes aren't stacking. Currently I've had Aqua Vitae, Aqua Fortis, and Aqua Regia refuse to combine stacks (what was just created won't stack with what's in the inventory). I literally just started up the game to look up the names of the items that wouldn't stack, then found that they would stack.....So it seems it's an unpredictable bug. Edit: It seems to happen every time, actually. The strange thing is that save-quitting and reloading the game fixes it.
Potions' ability to stack seems to fluctuate randomly from individual item to item. Sometime I'll have an Infernal Potion, and pick up a second one which refuses to stack with it. Then a third Infernal Potion will be willing to stack with the second one but not the first. It's all incredibly arbitrary. I've never noticed whether or not reloading makes them play nice with one another or not.
This is one side effect from using Cube artifact. Least one of teleporting tool does that. Check my activity for more info about it. Not sure which one and haven't really written all cases up.
