Married couple is only allowed to claim on one house, not one each, is what I understood.
She would have been OK if not married, then, because nobody would try to argue where she spent her time all those years ago.
Indeed. But, there are still two possible ways that she may not have done anything wrong as regards CGT. One is that a nomination was made that her house was the main home (unlikely, by the sounds of it, as she claims she had no knowledge of CGT rules). The other is that, as a matter of fact, her house was the main home for her and her husband. The evidence so far doesn't seem to support that. But we may not have all the relevant facts.