I would suggest that the smudge is deeper than the surface. It sounds like the wet varnish was unable to dry due to being against the braces and probably moisture due to humidity penetrated the varnish or there was off gassing from the foam that covered the braces. I have seen this happen before with customers boats when they try to varnish both sides of the kayak too quickly by turning it over before one side is fairly dry. It may go away with time as the varnish dries, but I think a deeper sand is require