This began happening Tuesday March 10, 2015. I installed the latest update for Grand Theft Auto V (the heists one) the day it came out at around 12:05 AM, which was March 10th. What's been occurring is my controller no longer starts up the Xbox when I turn the controller on (like it used to before I installed this update). Can a game's title update affect Xbox hardware? I doubt it, but this is the only cause I can think of since Microsoft did not release an Xbox One firmware update recently. Or if they did, I wasn't notified nor did I install it. Now, I have to connect the controller then turn on the Xbox manually. The controller connects and I can play the game with it, but other than that, the only issue is that the controller doesn't turn on the console. The console is only two months old. Anybody else have this issue?
There are a couple things you can do that might help.
As with dkiefer's answer simply turning everything off for a time could help. If not, try doing these steps:
Make sure your Xbox is still set to "instant on", You can check this in power and startup settings.
Update the controller itself, You can do this by navigating to device settings and follow the steps there.
Make sure your controller is correctly paired to the console. Press the sync button on the side of the console and the same button on the top of the controller. If you've recently brought the controller to play on a different console, or plugged it into a PC. You may need to re-pair it.
Check the power supply. If the light is not on, check your connections.
I've had issues with turning it on by voice. While the Xbox is on, turn it off and clear the cache by holding the power button on the console for about 10 seconds. Wait for a little bit, and then turn it on again by pressing the button on the console. Hopefully that will enable your controller to resume powering on the Xbox.