In the case that your controller is connected to your Xbox One, but the connection seems to be off. Then it's recommended to delete the connection for a moment and clear the cache on your Xbox One console for a moment. This can be done as follows:
- disconnect the controller from the console
- Turn the Xbox One off completely and remove the power cable for about 10 minutes
- Reconnect the power cable and fully start the console. Wait until you're at the Xbox One's main menu
- Login with your Xbox One gamertag/account
- Reconnect the controller to your Xbox One and then you should be ready to go!