I have an inconsistent but not infrequent problem with my controllers freezing/console won't take input from controllers. The packed-in controller and a Titanfall controller. One with headset adapter, one without. Both have the latest controller firmware update. An example: controller input doesn't navigate home screen, launch games or apps, invoke menus, whatever. Home button tap will sometimes go home as it should, but not further input recognized. Holding home button brings up turn console off or turn controller off dialog box as it should, but can't select either option, or the close option.
Interestingly enough, this also happens with the Xbox One infrared media remote. Same deal. Console won't take input from the remote, or the only input it will take is home button taps or holds.
Doesn't seem to freeze during gameplay. Only during app or home UI interaction. For example, controller won't freeze playing Borderlands: The Pre-Sequel, won't freeze in the game's pause screen or options screens, but open friends or chat during a gameplay session, controller input will freeze in the app.