Ah ok I understand you now. Make sure if you upload the game manually to create a single zip file or you can use alternative the buttler command line tool. Generally you should be uploading one file, a zip file, that compresses all other files. Other than that I cant see why Itch.io would have a problem with the number of files your game uses. Is it a browser game ?
1 year ago(+1)
Itch.io has a limit on the number of files, for performance reasons. I believe this is only imposed on browser games, but I could be wrong. In the case of a zip file, it counts all files after being extracted.