So way back before my hiatus I used to be able to dye my mutants in the springs. However now, it seems like no matter how many days I visit it never seems to dye them. Is this an update/glitch that I missed? I would love to have colored mutants but I don't want to keep wasting time at the pond.

You can apply dye colour dips to mutants. I'm pretty sure having a mutant selected can activate a colour change but if in doubt, select a regular pet and when you get a colour change, switch to a mutant to accept the change. ^^