I used to have 3 ice arrows, that add +1 cold damage.

Now, I picked up a stack of 10 acid arrows that did look identical, but had +1 acid damage instead (not surprising).

When I was looking for them to load them however I could not find them. Closer examination revealed, though, that I now had 13 of the aforementioned ice arrows.

Same goes for other ammunition that was probably fashioned from the same blueprint and/or has the same ResRef or the like, so all Dung Clods/Maggot Clods/Dung Balls become one stack, even though I think the kinds of disease they inflict do differ.

Not a problem per se, at least not for me, but I thought I better had it reported.

This is caused by different stackable items having the same tag. To prevent it from happening, the stackable items need to have their tags modified slightly so that they aren't identical to the tags for other stackable items.

I didn't make those items, and so I'm not sure where to look in our loot system in order to fix this, but whichever DM did should be able to track down the items and get the tags changed.

Same goes for smooth gem and round sapphire.

Whoever made those items -- is this fixed?

Pretty much. There may be exceptions which I'll notice with time.