I recently had this issue too.
== '''I fixed this by :''' ==
* '''removing my plug-and-play battery'''
* '''installing normal AA batteries into my controller'''
* '''restarting my xbox one normally (switching it off and on with the power button on the console)'''
* '''switching my controller on after my console had booted up'''
It turns out that even when charged (or plugged in with micro USB to my console), the plug-and-play battery was causing the issue. Removing the battery and directly plugging in my controller with a Micro-USB also did not fix this issue.
Posting this here in case this helps someone else fix this issue.
[quote]Note: this is not a guaranteed fix, but it solved it for me and is worth trying if other methods fail.[/quote]