Itch does not modify or alter the files you upload.
The problem is on your side and it sounds like you have something misconfigured in godot.
Try copying only the exe that exports godot (without uploading it to Itch) to another folder in windows and try to run it and you will get the same error.
Without any additional information, I have to guess, but I'm betting that you are testing your game from the Godot IDE and you are running a different scene than the one you have as main, hence the exe you export does not work.