There's no time-frame given for when the ending scenes take place.
The auto-pilot was fixed "six months ago," and I'd guess it would take a few, maybe even six months, for Gotham to get up and running again. It's entirely possible Bruce fixed the auto-pilot before getting whooped by Bane, or right when he got back from the prison.
Now that's a stretch. The autopilot thing definitely didn't seem like a five minute or overnight fix otherwise Lucious would have done it awhile ago despite how busy he was. Bruce had plenty of free time before he got his back snapped. While we don't know the exact day Bruce got back to Gotham, the timeframe for that is pretty narrow considering he had to come all the way from India and sneak into the city. Yea there's no real timeframe in this movie, it makes much more sense the repair was done before the clock was in the last stretch.