iPad 2 Smart Cover leaving black stains on the device!

I've got an iPad 2 and a Smart Cover that I use since I bought the acessory by the end of 2013. This iPad was traded at the Apple Store because the old one had its screen shattered, so Apple gave me a refurbished one in January 2013 (I bought the first exatly a year before the trade). On the old iPad I always used the Smart Cover, but I ended up losing it so I bought another one by the end of 2013 as I said. A few days ago, removing the Smart Cover from the iPad I noticed some black stains on the iPad and on the part of the Cover that attaches with the iPad. It seemed really odd to me so I tried cleaning with a moist cloth because I thought it was just dirty or something, but the stains refused to fade, which led me to think that is something related to the magnets inside the iPad and on the Smart Cover. Does anyone know why/how this happened? The stains LOOKS like burn marks, but I don't know...

Here are some pictures of the products:

(It even made a little damage like it was hit.)