Apple ID replaced with someone else's after iOS 6 upgrade (Security breach) I just updated my iPad retina (3rd generation) with iOS 6 and now my Apple ID has been replaced with someone else's ID. 



And its not jailbroken either. How did someone manage to do that? This is a serious security breach, I think.

I logged out of that Apple ID but how can I be sure that they are not tracking anything and won't be able to purchase through my account?
This is not as serious as it appears as signing into a device using a different Apple ID does not give one access to all the data on your device. What happens when you launch an app that you have officially purchased from the App Store? If it asks for the password of your proper Apple ID, then I would skip to the end of this answer and call Apple because that means the rogue account is actually signed in. If, however, it launches, then you are in fact logged into your proper account.

First, sign out of that Apple ID. Then sign into your existing (proper) one. Once done, sign out and then proceed to change the password on your Apple ID: https://appleid.apple.com/ as a proactive measure. And I would strongly advise you to use Apple's two-step verification if it is available in your country.

There exists no known way to hack into an OTA firmware update and hijack a system. iOS is actually quite secure. While I can explain how that email got there, I can say that it's likely an Apple server side error. Or someone local got a hold of your device and is messing with you.

Lastly, if you are 100% sure it occurred without explanation, I would contact Apple and not send emails to the iTunes Team, as they falls outside the scope of anything they can help you with. International contact info can be found here: http://support.apple.com/kb/he57