Melanochromis auratus is sexually dimorphic, this means the juveniles and females are one color, the yellow with black horizonatal stripes, however when the male is mature is coloration nearly turns the opposite. They will turn black with gold horizontal stripes. Now I am not sure if this is what happened to your auratus, or if it has retained its original color and that has gotten muddy. Keep in mind that cichlids change their coloration for a variety of reasons; blending in, happy, sick, fright pattern, feeding pattern, spawning pattern, etc.
As long as it is swimming okay and eating, I wouldn't worry about it. If it appears to be stressed or hanging out up in the corners of the tank, then you may have a problem.