Well, are they the same thickness on every disc? Does some discs have deeper scratches?
If it's a Wii-U only problem, and it doen't make it so bad that the disc stops working, maybe you'll just have to let it pass? Maybe you should take a blank CD, put music, or video on it, and try listening to music with the console flat, and on it's side. It could be a possition thing... Also, don't sit things on top of the console. Not saying you wouldn, but, there's people that do that.
Also, try to listen for a disc being scratched. You can hear it when it's happening. But, probably not when it's a light scratch. I say call nintendo just to be sure that it's something to worry about, or know why it's happening, then, take steps so that it doesn't happen as much.
