Xbox shut itself down while turning off in Instant-On mode

Go to Settings>Power & Startup and check Turn off storage when Xbox is off. That will turn off your external drive when the console is shut down. As for in Instant On mode I don't see my storage device on when the console is shut down.

Have you changed the power mode of you xbox so that when you turn it off it is actually turning off, and not going into "instant on" mode?

If it's set to "instant on" mode you can alternatively just hold the power button down on the front of the console for 5 seconds to completely shut down your xbox.

Here is a guide to the power settings, the different modes and how to change them

Update: It appears to be related to power-saving mode. If you don't use instant-on, when you turn off your console it automatically returns to Home while shutting down, thus the Last Seen: Home.

To turn off Instant On, go into the Xbox One’s Settings by pressing the Menu button, and then Settings, or say “Xbox, go to Settings.” Then go to Power and startup.

Select Power Options, and then switch from Instant-On mode to energy-saving mode. This will allow the Xbox One to completely shut down.

Turn it back on and go into settings and uncheck ""Xbox turn off" turns off my cable or satellite box"", then switch the previous setting back to Instant-On

It is a work around but the only down side is you will have to turn your cable/satellite box off until/if they get a fix

Do you use instant-on mode?

The RAM probably needs flushing and as instant-on mode is more like a PC sleep mode it wont flush the RAM when you turn it off.

So fully shut down the console for a couple of minutes.

To do that go into the power settings and switch it to energy saving mode. Next turn the xbox off.

After a minute or two switch the console back on and try the game again.

I've also heard that holding the power button down for and 15 seconds can also fully shut down the console although I've never need this.