I'm sorry to hear how your first litter turned out. It's always sad when these things happen. As far as "what went wrong"....
I'd "guess" either "temps" or "bacterial infection". Since your boa has never given birth before a bacterial infection "could" account for the strange color on the "infertal ova". After all, cages do get dirty during the breeding season. Normally we don't interrupt them just to clean the cage. So, build up of bacteria in the cage "could" happen. Even if your cage cleaning was done regularly it could still be bacterial. Of course, the main culprit would have been the temps in this case. If the temps are too low or too high she might have a larger amount of infertile ova. Some of this infertile ova might go "bad" inside the female. This could cause a bacterial infection. Although the mother wouldn't be adversly affected the babies would be. That would account for the deformed babies.
If you really want more insight as to what went wrong you should take some of the deformed babies and a few of the ova to the vet. They can run test to see if bacteria was present and get you a better idea of what went wrong. BTW since she did have a LOT of infertile ova it's a good idea to take her to the vet to get check. Especially since the color of that one infertile ova was so strange.
BTW I had a litter that was almost exactly the same several years ago. The female was fine afterwards. I breed her the next year and she became gravid/pregnant. Then the female died halfway through her gestation period. She died of a bacterial infection caused by "retained ova" from the previous year. A vet check after that bad litter "could" have saved her life. I just assumed she was OK. That assumption ultimately led to her death.
I'm not saying the same thing could happen to your female. I'm just saying it's possible and it does happen.
