So, ideally the traits were only ever supposed to work on independent ingredients/result items. When I first made the system that was the plan, but an oversight caused them to work with non independent ingredients as well. What was originally supposed to happen was that in order for an item to be on the 'additive traits' list in game successfully, it had to be put there by the dev in the plugin params, and also be an independent item.
Somehow, I'd mucked that second part up, and for a long time, you were able to have ingredients that weren't independent, but did have additive traits on them. When the other user I was talking about earlier reported a very similar issue, I realized it was possible in the first place to have additive traits on non-independent ingredients, but rather than fix the problem by disabling those traits on non-independent items, I "fixed" the problem he reported.
As it turns out, my fix likely only worked for ingredients in the first slot. During the function that combines all of the traits on all of the ingredients, the traits of the result item were being added to an ingredient, which would never have caused a problem if the ingredients were independent items. The item that would inherit all of those traits would normally be removed from the inventory after. However, if the ingredient was non-independent, all instances of that item would inherit the traits. The instances already in the player inventory, the instances in the shops, the instances in treasure boxes. If you then make the same recipe again, that ingredient has way more traits than intended, and adds them all back onto itself a second time, causing the bonus to increase again.
Worth noting, is that those traits aren't saved on the item, so if you saved the game and then reloaded a save and crafted the same recipe again, it would be normal again.
The fix I applied to solve the problem originally must've only been for the first ingredient, or the first slot, or both maybe. I'd have to look more closely at what I did originally, to solve this problem for you, or find a better way to more permanently solve it.
-Ramza