If the fillet itself is near or at legal minimum length just leave the skin on and you are OK. If the fillet is from a barley legal fish then you are pushing it and could run into problems.
They need to be able to determine the species and be sure it was a legal fish. I've actually left a patch of skin on the fillet and never had any problem. If I could not prove the fish was of legal length from the fillet, I just gut it.