For this particular issue it seems as if the resolution is more focused around what is actually pulled up on the screen. If you see "Favorites, Recents Contacts, Keypad, Voicemail" at the bottom of the screen it seems as if you actually have the phone application pulled up. Where you wont end up hearing or noticing any actual changes to the call or automated system
The resolution is seems to be where you exit that screen and go back to the Home Screen (Where the apps are) > at the top there should be a green bubble around the time or a green bar at the top of the screen.
By selecting this it is pulling up the active call interface. Where you can then see a variety of options. The focal point for this issue is the keypad, so you would select the keypad.
The main take away is that if you are accessing the phone app while on an active call, the phone is assuming that you are trying to make another call but not actually interacting with the current active call. To interact with the current and active call you would have to select the green bubble or green bar at the top of the screen.