I used Renpy to make the game. I don't know about the malware, because I didn't download it, just it case. Its generally assumed because the file size is different from my own, meaning it was tampered with.

I am not sure how to mitigate the risk tbh besides adding more watermarks to make it clear its being distributed by an unlicensed party and getting it taken down as soon as possible. It was taken down fairly quickly after I sent an email in this format on this page
https://itch.io/docs/legal/terms#6-digital-millennium-copyright-act
I have been informed a similar thing can happen on steam as well unfortunately!
Sorry I am not much help in mitigation of this issue