Lately I'm seeing this happen quite a lot. I have two XBOX One units and they both do it. I'll press the XBOX button to turn on the Unit and instead of that the controller light will just flash until it times out. It doesn't matter which controller I use (I have two for each) they both behave this way. The only fix is to restart the XBOX One.
As I said, it happens on both of the XBOX One machines I have and they both require a restart before controllers will connect.
It doesn't happen EVERY time, but it does happen quite often. Is anyone else seeing this?