Mine had this issue. Luckily Gamestop had some in stock and they exchanged the whole unit. I think the way Nintendo is asking for the complete return is far from the respect they should give their customers. They should ship a replacement dock and let us return the faulty one once we have the new in hand. Like any company that cares about the user experience would.
Sending in the whole system seems like an intentional deterrent to getting service. That's like sending in your entire laptop because it shipped with a faulty charger.