It sounds like when you are hitting your URL, you are not actually invoking a backend instance to handle it.
From the docs:
A backend instance can be targeted with HTTP requests to
http://[instance].[backend_name].[your_app_id].appspot.com, or at your
application's custom domain. If you target a backend without targeting
an instance using http://[backend_name].[your_app_id].appspot.com, App
Engine selects the first available instance of the backend.
The Backends API provides functions to retrieve the address of a
backend or instance. This allows application versions to target
backends with requests, for a backend to target another backend, or
for one instance of a backend to target another instance. This works
in both the development and production environments.
The BACKEND_ID and INSTANCE_ID environment variables contain the
backend name and instance index of the instance handling the request.
Modify your url to include your backend name (from you backends.yaml) and you should be able to access it, provided other configs are correct.
More on that same topic:
Backends share the handlers defined in app.yaml with the main
application version. You can place your backends in a separate
application root directory if you want to avoid sharing code or
handlers, or simply mark the relevant handlers with login: admin.
It might be helpful if you posted your backends.yaml, app.yaml and handlers if you would like a more in depth answer.