You're wiping metal off, I think the black part is a reaction with the cloth. It does the same for stainless steel on watches, even if you clean the watch beforehand anywhere you wipe turns black.
I just got a pair of Air Max 1 Anniversary Royals from StockX a few days ago, and the toe box looks a bit off compared to my Obsidians, Reds, and Aquas
Would you dudes mind taking a look at the imgur album and lemme know what you think?