I remember reading somewhere that some percentage of the time, the offpsring will get one parent's (or the other's) exact coloring, i.e. there will be no blending.  If that's not the case, then you might just have gotten a blending on the green toddler closer to the green father's intensity.  Does that couple have any other children?  How do they look?

It's probably because when you make your red/blue/green families, you make them the vary darkest shade of that swatch.  So when a blue and a green breed, there's no variation in the intensity of the shade between the parents, so all green children are the darkest green and all blue children are the darkest blue.  And when a r/b/g sim spawns with a flesh-colored townie, the townie is likely not to be the darkest possible in their flesh-colored swatch, so the children will have some color variation in the r/b/g swatch.  It's working as intended.