can you provide more information about how did you created the zip file?

It seems that when your zip file is unzipped it contains additional folder which is zipfilename in your case.

You can solve this by zipping like this:

# go to your application folder
cd ruby-app-folder
# zip everything recursively and create app.zip in parent folder
zip -r ../app.zip ./*
# go back to folder where the zip is created
cd ..

Then when you deploy through "Upload application version" the application should be unzipped correctly.

Can you try that and confirm my assumptions?