I think i understand your situation.
I still have this problem with the newest commerce kickstart2. I think the problem may because the separation of products and products display. For some reason(crash of the program, or cancel of the operation in the middle of the process...), it happens, there are products in the database but the product is not shown in the admin panel/ mange products. Therefore, when user try to create the same product (SKU) he can not see in the mange products, system checked the database and tell there is only this SKU.
If you want to use the same SKU, i think you have to go into the database and manually find that SKU and delete it, then create you new product with this SKU in the admin panel/mange products again. At lease that is what I did.
Maybe some one can come up with a deep understanding and reason for it?