Yes, using the app.yaml file, you can set the type of scaling that is used by your App Engine app. You can specifically see the reference on how the scaling elements are to be syntactically added in your app.yaml file. Since this file contains the specifications for the deployment of your app, it would be the proper place to change the settings.
Have you recently encountered this issue? There is currently an existing incident that is affecting multiple Google Cloud products which could be related to the errors you are seeing.
Were you able to change your App Engine settings the way Ernesto suggested?
The issue ended on May 6, as you can see in the shared link, and App Engine was not affected.