I had the same issue, I updated the firmware on the controller and then restart everything, this fixed the problem. The problem seems to be known to Microsoft as it's on the front page of their controller support area: https://support.xbox.com/en-GB/xbox-one/...
Instructions from site:
1 Sign in to Xbox Live on your Xbox One console and install the latest system update if prompted to do so.
2 If you have a stereo headset adapter, plug it into the bottom of your controller so it can also get updates.
3 If you're using a stereo headset adapter, plug in a headset (a headset must be plugged in so the adapter will turn on).
4 Press the Xbox button to open the guide.
5 Select System > Kinect & devices > Devices & accessories, and then select the controller you want to update.
6 Select Device info, select the Firmware version box, and then select Continue.
7 When the update is complete, you can update additional controllers.
They provide instructions on how to update via USB and PC if this doesn't work.
Hope this solves your issue!