Spots in Stainless Pots after cleaning in self cleaning oven
A self cleaning oven won't clean pans put in it, only the bits of oven wall that have the right surface and get hot enough. If the pan you put in was dirty, all you've done is burn the food on to it. 

Stainless isn't a finish, it's a material, so you may be able to remove the discolouration by polishing or sanding it. But if you make the surface rough, food will stick to it.