To answer your question, yes...identical twins would be the same color. This is not a case where the embryo split. While they were both heifers--identical twins are always the same sex--identical twin calves would also have been the same color...either both black or both red.
Your twins are then "fraternal" and the result of two separate eggs. There is more than one possibility of how this could have happened, and I'm not sure of the likelihood of each, but here are a few possibilities...
I agree with one poster above...there is a possibility that there were two embryos in the straw. Hopefully, a competent vet or embryologist would have caught that either when they were frozen & packaged or at thawing for implantation, but I dunno. We don't do a lot of flushing, and I'm not sure how often this happens or how easy it might be for somebody to miss an extra embryo in there...I would say it's possible, regardless of how good somebody is or how much experience they have. And I would guess the possibility of something like that increases with a lack of experience on the part of the person who recovered the embryos.
Another possibility is that your recip cow was bred by natural service BEFORE she was implanted, meaning the twins could have been hers. Are you absolutely sure there was no contact with a bull BEFORE she was exposed two weeks after the ET?...which I'm assuming was 3 weeks after her heat. If a bull got to her that day, she would have been due the same day as the embryo, and this scenario seems a little more likely to me than the likelihood of having two embryos in one straw, but that's just based on my experience and the reality that things like that do happen, regardless of the best of intentions.
A third scenario, and I'm not real sure how possible it would be, but you might ask a good embryologist...would it have been possible she was exposed and got bred AND conceived with the embryo that was implanted? If you know enuf about the genetics of either the recip or the ET mating to know that either a black or red calf shouldn't have been possible, this would seem like a possibility to me. The part I'm not sure about is a cow that has conceived maintaining a pregnancy--even for 8 months--if her uterus was entered into 7 days later to deliver a second embryo...I don't know that.
I would say if you want the seller to make good on the guarantee, you might go forward with the genetic test. If you can prove that these calves ARE NOT a product of the embryo mating, then they should compensate you according to the guarantee. If either one of them IS an ET calf, I think the contract was probably satisfied and it's your loss. Nobody guarantees a live calf...it's usually a 60 or 90 day pregnancy. In the case that BOTH calves are embryo calves, I personally would expect a breeder who provided that embryo to want to do something. If that's what happened, it shouldn't have happened, and the responsibility is on the embryologist.
Hope that helps. Sorry about the babies. Good luck!