I've never had a parrot before that DIDN'T develop "smudges" on its body and fins....
It's part of the color of the fish, but it doesn't manifest itself until a little later in life. I used to freak out over it, until it happened to more than one of my parrots (I've grown out about 9 of them total in the last 4 or 5 years).... there was nothing wrong with my water, and the tanks were WELL established.
That clear color that comes from the dye process (for artificially dyed fish... I have only ever owned one such fish) will fade in time. What starts out as a wild flourescent color will fade eventually down to the fish's original gold or orange color, most likely with streaks, stripes, spots, or smudges of stark black over the body.