If an iPhone is being damaged in the box, the box will be damaged. What's happening is that a small number of units were damaged during assembly, and weren't noticed during the QC processes (which typically, and realistically, involve spot-checks rather than full visual inspections of each unit).
As well as the Nanos sold, they weren't produced in numbers so large (or quickly) as the iPhones are during the short pre-launch period. When you have to prep 5 million of something in a few months, there are, inevitably, going to be some failures in the QC process. It happens with *every* device ever made, including those which are much more expensive than a phone.
I still remember back with the release of the iPhone 4, when people complained loudly and constantly about how easily the glass scratched. Then came the videos of people showing off their damaged phones. Then came the videos of people trying (and failing) to replicate the damage in a manner consistent with the way people described their phones being damaged. (Scratching it with keys, etc.)
Now, just over two years later, we're back at the beginning of that cycle, and everyone is complaining about how easily scratched the aluminum is, even though there were no such complaints for the Mac Pro, iMac, MacBook Pro, MacBook Air, or iPad. Or, as you pointed out, the iPod Nano. All of those have anodized aluminum shells (though in the majority of those cases the anodizing process isn't being used to add a color).
Face it, the iPhone 5 is significantly more scratch resistant than the vast majority of smart phones on the market, with their plastic shells. If they *hadn't* anodized the aluminum shell, it would actually be *SOFTER*, and more prone to scratches and dings.
Note: Personally, I'd prefer a black iPhone with an uncolored (silver) aluminum shell, but that's a purely visual preference and not due of any potential scratching issues.
