The only way to get control of the console was to reboot it, however I now have a work around which involves the power mode settings. I believe this is where the issue is. To stop the controller freezing do the following:
First switch from instant on to energy-saving mode on your Xbox One.
Press the Menu button on the controller. Go to Settings > Power & start-up, highlight the Power mode, and press the “A” button to select energy-saving.
Once done go into Network > Advanced settings > Alternate Mac address, Clear that and the console will make a restart. Now use your Xbox One for a period then leave it alone for around 10 minutes, you should find the XBox One controller no longer freezes, hopefully this will be fixed in a firmware update.