From what I've found people's best idea is that this happens with clip studio and some other select program because they handle antialiased/semitransparent pixels differently, making them read as white instead of black in certain programs such as PNGTuber Plus and often discord.
The weirdest thing here is the fix - open each individual art file you use to piece together the model in Microsoft Paint (it's weird, I know), hit Ctrl s to save, and close paint. You've fixed it! It's how I've been fixing all of the models I rig and it's been working a treat, even if it is boring and repetitive.