Generally, you want the Color Catchers to not end up full of dye before it goes in the dryer. That said, low heat should not have set the dye if the change was due to the black bleeding. In that case, you should be able to pop it back in the washer with some more Color Catchers & just re-wash (I don't ever wash commercially dyed fabrics on anything but cold).
There are 2 other possibilities:
1) It was not bleeding, but crocking. Crocking is more common in prints than solids & happens when 2 fabrics or parts of a printed fabric with different colors rub against each other. I've not heard of any reliable solutions for treating crocking. If your fabrics were all solids, you could use Synthropol, followed by Retayne to properly set the dyes where they currently are, but that doesn't work for printed fabrics.
2) If you didn't pre-wash your fabrics, it's possible that the colors actually did "fade". I'm not sure what brand of the comic book fabric you bought, but I typically see those produced more for big box stores, than for LQS'es. Often they will add a chemical coating to the fabric that makes colors look more vibrant ... until the first time they go through the wash & the chemical coating is rinsed away.
Here's hoping it's just that some of the black bled in the wash. But even if you can't get it back to the original bright green & yellow, kids are very forgiving & it's likely they will absolutely adore a quilt made with their favorite characters and won't even notice the color change that seems so glaring to you.