Looks like a faulty dye problem so it won't affect the cpu or anything else... But looking at your picture I see that the two bottom corners are bent, which means the top of the cpu plate is not flat. THAT is a problem since the heatsink won't be able to sit flat on it and it will heat more than necessary.
Some people likes to polish the heat plate themselves. Doing that it would make it flater and remove those markings. Do so at your own risks tho. (so why did I mention it then? o-O)