Interesting. I assume you are on the latest code. What control scheme are you using to pick this stuff up?
I'm trying to find patterns. So far it only seems to happen when dropping items into a container without opening it, and only certain items. It also doesn't affect the weight of the stack when the items are duplicated. I had a stack of over 80 fish that only weighed one stone. So far I've duplicated gems, coins, some food, keys (this was the first clue something was up), lantern oil... I couldn't get it to work on the flying potion in level 2, or some of the other potions and scrolls. I haven't tried duplicating explicitly non-stackable items like equipment yet.
Huh... It's like the cursor remembers how many objects are in the stack most recently drag and dropped until a container is opened. I started with a stack of 30 sling stones that I dropped into a container. Then I picked up 3 individual stones and dropped them, one by one, into the same sack (it doesn't seem to matter if it's the same container or different ones). When I opened the sack, there were four stacks of 30 stones.