How did you configure the custom domain and the SSL certificates, exactly? A step-by-step description would help a lot. Have you followed any document?
After you set up your custom domain and update the DNS records, a managed SSL certificate is automatically provided within a few minutes. Have you verified that the SSL certificate has been actually provisioned? You can do that by running:
gcloud beta app domain-mappings list
You should see a list of your domains, subdomains, and all their corresponding certificates, for example:
ID SSL_CERTIFICATE_ID
You can gather more relevant detail from the "Securing Custom Domains with SSL" documentation
page.
Any other piece of information you deem relevant might prove of great help.