This app is not compatible with my phone, but my wife uses it. With this you can check how many “nikuvim” have been used on your RavKav (and where and when they were used) so presumably it should be fairly simple to know if the train is taking an extra ‘nikuv’ or whether it is simply a different counting system.
The app is for android.
This developer also has an app which says when the next bus is coming (it works in Jerusalem, not sure about other parts of the country).
Let me know (via the comments) whether this app says that CityPass is taking extra money or not.