Xbox Controlller Not Shutting off after console shutdown

I changed it to never turn off , but I’m playing games when it freezes . I’m not just letting it idle or turn off after media. The console seems to freeze after 5-6 hours of playing , then shuts down and I have to manually turn they system again again. When the console shutdowns the controller stays on.

As for the downloads on 360 they would continue to download after you shut it off, just like the controller would continue to charge after shutdown (which I haven't tested yet on x1).

If you turn off the background download option, the Xbox turns off instantly. Only with backgrond downloads on, the console will sync your Gamertag, or finish any downloads still queued, and will then shut down completely. So if it bothers you, simply turn
off downloads in the background.

Despite (not) using Cloud storage, your Gamertag is now saved differently online, so you can recover it to multiple consoles. I guess that's the reason why the console is now up/downloading stuff after shutdown after the latest update.

The light flashes when the console is downloading content from Xbox LIVE. If the console is in the middle of downloading something and you shut off the console, it will still finish the download. If you want the console to shut off without finishing downloading
content you can turn off background downloads. Navigate to Settings > System Settings > Console Settings > Startup and Shutdown > Background Downloads and click "Disable". Hope this helps!

Alongside PollockRoc's suggestions:

1. Never push your disc tray to close it. Either push the button or close it via controller. Doing this will insure that you don't accidentally damage the tray.

2. When you turn off your Xbox, be sure to dashboard first. Look at it like shutting down a computer without using the proper shutdown procedures. It hasn't been proven definitively as far as I know that shutting down mid-game does any long term damage,
but better safe than sorry.

3. Turn on the auto shutdown. If you ever forget to turn off your console, the auto shutdown will turn off your console so it doesn't get left running for an extended period of time.

Hopefully this helps, enjoy your box!