It was apparently his old dog, being replaced by his new dog. The Skinned Hound will be reanimated after the completion of the quest "Ushnar's Terror "(a quest unavailable to Khajiit players, as the Orc is afraid of cats) and will follow the Hero until death. It is not possible to tell the Skinned Hound to wait, and it will not respawn.
If the Hero fast travels, the Hound does not travel along. Instead, its Speed is temporarily increased to 255 to catch up with the Hero.