I've had this happen now with thieves tools and potions.
Incident 1: I had picked up a number of thieves tool packs, about 8 in total. 6 grouped automatically, but two others remained obstinately separate. By sending them to another character's inventory, one of them grouped - and then crashed the game to the desktop when I tried to move them back to the main character.
Incident 2: I had gathered potions of speed as I traveled, about 5 in total, found on Illithids and in various other locations, and noticed that 1 potion had not grouped with the others. The stack of 4 would not split, and could not be consumed. So I sold them off. But that was a weird effect.
