Most refurbished cameras are returns from buyers that had buyers remorse, had unrealistic expectations for the camera's performance, or because of ignorance thought the camera was malfunctioning when it wasn't.
A much smaller number are returns that needed some kind of repair because of a defect in materials or workmanship during assembly. A few are cameras used in the factory for various purposes or that were on display at a Nikon booth at trade shows.
Refurbished cameras that need it are returned to like new condition but because of legal issues cannot be sold as new.
All refurbished cameras get individually tested for correct functioning and calibration, but with new cameras only a random sampeling gets individual testing.
Nikon's warranty only applies to the original owner, but Nikon warranties the cameras they refurbish for 90 days.
Used Nikon cameras have no Nikon warranty because the warranty only applies to the original owner. Some camera buyers purchase 3rd party extended warranties that may, or may not, be transferable to a new owner.