So I just used a mutagen on  http://beastkeeper.com/pet/5156, but it looks like something weird happened.

Before I used the mutagen, her muscle genes were both Normal Muscles. After I used the mutagen, though,  it said that the Normal Muscles were changed to Spitting Muscles, but when I went to check her genes it now says she has the Dystrophy gene and the Spitting Muscles gene. So is the mutagen supposed to change both genes of a type or only one? Because  I never got the message that one of the genes also changed to dystrophy, which makes me pretty sad because my pet now has two red stats and before the mutagen she didn't.

should be one per mutagen as far as I know

According to the 4 AM database dump, your dragon had Dystrophy before mutating. Normal Muscles gene has more genetic power than Dystrophy and it wasn't expressing. After mutating Normal Muscles to Spitting Muscle, Dystrophy became dominant gene because it has more genetic power than Spitting Muscle.