Unfortunately, I know apple will not replace this or help to fix this problem with the smart cover because I have called and talked to them. Only if you had bought a warranty with your iPad I'm sure they would be GLAD to fix it. Im having the same exact problem though, and believe me I know!.. Its aggravating.
It almost looks like its leaking the magnet or whatever the black stuff inside of the bar on the protector is on top the side of my white iPad (silver), so it is very noticeable. Every now and again I get some water and a paper towl and get it off, but you can still see very faded black dots where it leaked onto my iPad. It started off with one black spot, then the other end started leaking, right where the bar pivots. And then where the actual magnetic strip is I have multiple lack dots, but they don't leak. So I'm beyond frustrated. I'm about to buy a nice silicone or leather case for this bad boy and call it done.
Probably going to trash this "smart cover" very soon.
Sorry, but there really isn't anything you can do at this point but get a new protector.
Hope this helps!