Hi Dimitry,
A workaround was found for this issue.
The problem was that the "old versioned" instances were still running, so upon deploying a new version of your app, specifying the version ID as the "old version" like so [1]:
gcloud app deploy --project PROJECT_ID --version VERSION_ID
the old version will be moved to "stopping" state as the new version takes on "starting" state with the previously used version ID. Try the following to resolve the issue:
1. Filter version IDs of the "zombie" instances from the logs
2. Then deploy the new version with the version ID of "zombie" instance.
3. If you have a script for automating deployments, reconfigure it to use fixed "version ID" to prevent same issue in future.
Once deploy, you should notice in the dashboard's "instances" view the result of the recent changes. If this doesn't resolve your issue, then provide more details on your method and description of the behavior in our Public Issues Tracker tool and we will investigate the issue further there [2].
I hope this helps.
[1] specifying version:
https://cloud.google.com/sdk/gcloud/reference/app/deploy#--version