So I've been experimenting with the mutagen and it seems to be working alright. However my Puma changed colors it would seem, from Yellow to Brown. He looks brown now, but the eye color was yellow before:

http://beastkeeper.com/resources/pets/cat/a5_b3.png

After:

http://i46.tinypic.com/az8dg6.jpg

Is this a bug or is this just how it works?

Well since color is also a gene then yes when this gene was changed you would see the effect by its fur coloration or pattern when the pattern gene would be affected.