When the technicians are talking to Lucius Fox about Bruce Wayne fixing the autopilot at the end, they say he did it months ago, meaning that this secondary Bat (the grey one, not the black one Batman used and destroyed in the nuclear explosion) was in the Applied Sciences facility at the time when Bane broke in and stole all their equipment, Tumblers, etc. So why didn't they take the grey Bat as well? Not only would it be their most powerful weapon, but they'd be able to fight Batman in the air, as well as transport the bomb in it, as opposed to on the ground, making it much more difficult for the cops and Batman to secure.

Also, someone on another discussion board brought up the fact that the ending shows Bruce Wayne confirming he's still alive to all four friends, not just Alfred. Sure, Alfred actually bumps into him at the restaurant, but Gordon sees the Bat signal on the rooftop fixed by someone other than him, then looks over his shoulder. Fox realizes that Bruce is still alive because of the whole autopilot thing. Finally, Blake gets a note from Bruce, with the directions to the Batcave.