Try not to worry too much about young fish changing colors. My ryukin is 4.5" and 2 months ago I freaked out thinking he had some kind of fungus. Slowly but surely a patch of his scales turned a nice black color. Now more are following, but its definitely just coloration.

Something important though, you said it's a small tank. How small is it and how many "feeders" do you have? Its a common misconception that these fish stay small and thrive in small setups. You and your son may be better off with tropical fish or a betta. While goldfish are hearty,they require a lot more space if you really want them to grow and lead a decent life.