I assume you tried wiping those marks off. I've seen those marks on every system and it's simply skin oil from using the touch screen with hands, then the bezel touches the top screen. On my OG, I would even get a circle on my top screen from the circle pad. I've never seen any of these marks become permanent, and that is after years of use, and even two child-owned systems do not have permanent damage. They all wipe clean with a cloth.
We have two launch blue and black systems and I still don't see any marks. We don't even use cases on the OG systems, as they are nicely self-contained and the case plastic is durable. The XL systems need babied, though. Although the new XL has the OG style case plastic, so I am much more confident.