I assume you shipped the body to Nikon and knowing the ability of some of the shippers to bounce your box a few times while it is in transit it could have impact damage when it arrived. I would just file a claim with the shippers insurance carrier using Nikon's report that the body had experienced impact damage as documentation.
This might not be as easy as it sounds. My camera's first time to service I was told to pay (for defective still under warranty D800) and it ended up being $180 for shipment - insurance only works if carrier personnel packs everything according to their rules.
Hopefully OP has bought this insurance and has followed all carrier procedures. In any case this is not going to be a fun experience. Sorry.
I've had two bad experiences with "impact damage". First was 10 years ago when I sent my camera to El Segundo for a "free" cleaning. Dust on the outside does not impact the camera. At that time there were many others of us that were asked to pay so I think it was a management scam. I had to resend the camera to Melville because they messed up all the adjustments in California. It came back from New York better than new (no charge).
Second is when I sent my 70-200 in for adjustment. There was so much impact from shipping that the filter and end element were broken. When I put in a claim against the insurance I paid extra for, USPS said the camera was sent for repair therefore it must have been broken before hand and refused payment. I would never send anybody broken glass (even if I hated them).
Sorry to hear about this.... I've used El Segundo a couple of times for the D7000 I had, each time I personally dropped the camera off so as to avoid any shipping issues like this..... I have thought about sending in my D800E for the left side focus issue but haven't had it bother me enough to do it. I try not to use the left side points much. Anyways let us know what comes back in the mail... maybe a couple pics of the box un-opened and then opened so you have proof of the condition you received the camera in.....
Wow, seems Nikon has been dropping the ball a little with customer service lately for some reason......