I removed some temporary roof underlayment on a small part of the roof to put on what was supposed to be there

The temporary paper was there for about 2 weeks with a little moisture under it, that new look the plywood had is gone now and has some dark spots and dark patches on it, is this just cosmetic surface discolor or should I clean it before I put on the permanent underlayment? This is only on like 5% of the roof the other 95% is perfect