Mine did the same thing! i updated through wifi the Apple was went to the end then said plug into iTunes. When i plugged it in iTunes said its in recovery mode and the only option was to restore or basically wipe my phone! So i went for it and iTunes ran through the whole process then it said could not be restored, error! it still says plug into iTunes?!?!?!
I updated my iPod Touch 4th Gen to iOS 6 manually through iTunes and even jailbroke the idevice. Here is a trusted website to download iOS firmware if anyone is interested: http://www.felixbruns.de/iPod/firmware/