There’s a chance the Itch.io app can’t recognise which file is the executable one. Do you happen to have multiple executables on the same directory? Or is the main executable missing from the root directory?
Itch has the App Manifest which you can include in a build, to let the Itch app know which file to run for what purpose. I haven’t tried it myself, by maybe you can give it a go?
On that note, have you tried running your game yourself from the Itch app? If you get the same error, that would make it easier to fix.