It depends on the colorant. It looks like the color is clumping with some of the bath bomb mixture and is not being distributed evenly. Are you mixing with your hands? The colorants I used in the past blended beautifully and the colors I'm using now has speckles, but hey, I think it adds character to the bomb. Maybe that's just me though...
I think but could be wrong, but because there is so little liquid used, that it is moisturizing a bit of the colorant and that is the darker spots. This is just a guess.
Can you guys recommend a colorant that you've had non-speckling (lol) success with? I was using the Wilton gel cake coloring. They don't speckle at all 'til around 4 days later.