I know the show came out months ago, but I still have to complain about this. It makes no sense for Madelyne to be in X-men 97. First off, it breaks the canon established in the original show. Jean looks into Cable's mind, and it's implied that she knows that he is her and Scott's son. Cable also implies as much when he says they can skip Jean and Scott in a review of the X-men. But, what really bothers me isn't actually the breaking canon, but instead how it doesn't make sense for Madelyne to exist.
In the comics, Sinister creates Madelyne after finding out that Jean has already been discovered by Xavier, and thus will be unable to get Jean into his mutant breeding plan. And the clone doesn't work until the a piece of the Phoenix enters her after Phoenix Jean dies on the moon. Now, if Jean had died in the original XTAS, and Sinister had created Madelyne to breed with Scott then, it would make more sense for Madelyne to be there. But, she doesn't die in XTAS. Thus, there is no reason for Sinister to create Madelyne. Scott and Jean will have his baby naturally. He doesn't have to get a clone in there. But, for some stupid reason, he decides to switch Jean and a clone. Why? There is no logical reason for him to do that. And Sinister is a logical person. It's an out of character moment that defines most of that season.