You could report this issue here[1]. You could also make sure you deleted those versions[2]. Take a look at this post[3] where it is explained how to clean up an App Engine project.
[1]:https://issuetracker.google.com/issues/new?component=187191
[2]:https://cloud.google.com/sdk/gcloud/reference/app/versions/delete
[3]:https://medium.com/google-cloud/app-engine-project-cleanup-9647296e796a