It seems in iOS 6, a drop shadow is automatically added to the navigation bar even when you set a custom background image. I\'m pretty sure this wasn\'t the case with iOS 5
General, non-NDA-infringing answer:
If you don't want something sticking out of a layer, mask the layer to its bounds.
[self.layer setMasksToBounds:YES];
Set the height explicitly to 44 (or 32 for landscape on iPhone) if that doesn't work on its own.