For some reason some things just don't stack, even if they're labelled the same. Human bones stack only based on the culture the bones' former owner belonged to, for instance. Arrows similarly end up in multiple stacks of arrows labelled the same, and I think I've had 3 different stacks of hand axes.
There are also cases where things don't stack temporarily, such as e.g. having an empty bowl in the inventory and eating the last food in another: they'll show up as two separate bowls, but stack when dropped.
A third case is with plants, where leaves from a plant stack differently depending on whether the threshed plant was flowering or not. I think picked leaves end up in one of those two categories.
Curiously, things that did not stack earlier did when UrW was upgraded. I believe I had water skins that did not stack before, but did afterwards (the water skins were spoils either from wounded adventurer quests, Njerps, or robbers, as are all my water skins except the fine one have been acquired: I made the fine one, and haven't bought any).