You should be reporting this error in the
ongoing issue, eventually re-opening it, if you have good reasons to think this is an App Engine issue. This should allow Developers to examine your issue in depth.
It is advisable to run gcloud components update first.
What is the output of gcloud info?
More information becomes available if you run: gcloud app deploy --verbosity=debug. What is the output of this command?
You should edit out all private information from your reply, such as project names.