Controller Pairing issues can happen if for some reason pairing between the Ouya was lost due to factory defaulting your console or possibly the controller had its battery left out for a while. It can even happen to other environmental factors such as a laptop with a actively sniffing Bluetooth chip taking control of the joystick! Sometimes its to simply break the pairing with one Ouya so you can move it over or another.
I notice a lot of people come to my site for various support topics for the Ouya and I figured that I should make an article dealing with some of the Ouya Support in terms of troubleshooting issues that were simply too small to exist under one article. These are questions which pop up time and time again in forums as well as on reviewers that decide is a fatal flaw of the console. Just a kind note that your Ouya has a 1 year warranty from the time of your purchase to be sure to keep that sales receipt in case something catastrophic happens to it.