Hi,
I had the same problem you mentioned. You should try this workaround:
1. If the web app asks for creating a feature service, click ok, then close the app builder and open your web map.
2. Now it contains two feature services, the one you created from the csv, and the one the app created.
3. Delete the feature service which was created by the app automatically and save the web map.
After this the app builder recognised my own feature service.
Ákos