Hi. Yes.
My files were correct on local system and GitHub, but not on PythonAnywhere. What worked for me is the following:
1) Go to BASH Console on PythonAnywhere. Enter the command:
rm -rf <your-repo-name.pythonanywhere.com>
2) Go to Dashboard -> Accounts -> API Token -> Revoke and Generate new API Token (I am not sure if this is required, but I did it just in case)
3) Now you can get repository from GitHub to PythonAnywhere by NUKING the old running domain
pa_autoconfigure_django.py https://github.com/username/repo.git --nuke
4) Your github files will be now in pythonanywhere. And Virtual Environment will be created in the Bash console