I had this on my first iPad and smart cover (I have been through 3 iPads and smart covers - long story).
Basically, the anodised or painted coating on the smart cover hinge was rubbing off, and so it was basically metal from the smart cover, rubbing against the metal of the iPad. On mine, it was on the hinge area of the smart cover at the top. I took it into the store, and had the smart cover replaced. Problem solved.
If I had left it and let it continue, it would have eventually started scratching the iPad.