That's the first I've heard, probably anti-virus software reporting a false positive. I promise I haven't put anything malicious in there. Nearly 14,000 downloads and no complaints about trojans so far.
Doesn't the site itself, i.e. ItchIO check the files on their own servers for viruses, too? That's where it's being downloaded from and opening and checking inside a zip isn't exactly cracking the processor to do once when the file is uploaded... That's definitely gotta be some halucination by your software.