I should have added that to the known issues, but I must have forgot. Unfortunately, there are a lot of edge cases that aren't currently covered by the mod that would require a lot of work to fix due to how limited the modding API is. In this case, recipes can't have optional ingredients in this game, so the only way to fix this issue is to either add thousands of conditional recipes and somehow figure out the code to switch them on the fly or keep track of quality items and swap them back to their originals based on where they are.
Option one would massively inflate load times and doesn't really seem feasible at all while option two would have a UPS impact, something that I, as a very inexperienced Factorio modder, wanted to avoid entirely out of fear of creating a lot of lag for people.
The current situation essentially predicates on the idea that items that go into your inventory are used for building, whereas items for crafting should stay within their given chain of logistics and crafting machines. Obviously that is not ideal.
If you're wondering why quality items are even a thing at all, there's two reasons. First, it shows the quality stats in the inventory, which is nice but ultimately not needed. Second, belts have a ton of hardcoded logic behind how they're placed, and if you simply replace entities as they're spawned, it causes belts to freak out, placing undergrounds all over the place. If you look at the known issues you'll see a bunch of fixed issues there relating to belts. Creating quality items fixed those issues but also has side effects, as you've noticed.
Fixing all of these issues is probably possible, it's just that I'm very new to Factorio modding (this is literally my second mod ever, and it is an offshoot of my first mod ever) and am most definitely out of my depth here. The last thing I want to do is fuck up peoples' saves or cause UPS problems so I'm taking these more finicky issues very seriously.
Also, please don't feel bad about bringing up issues. This mod (and Better Quality, for that matter) has become significantly more robust as a result of people posting various issues and incompatibilities with mods, and I've learned a lot in a very short amount of time as a result.
