What is the ruling on a husband having sexual intercourse with his wife while she is observing a supererogatory fast, knowing that she is also making up missed obligatory fasts?

There is no sin upon you for breaking a voluntary fast, though it is better to complete it. As for your wife, if she fasted with your permission, it is not permissible for her to break her fast nor to obey you in doing so, because Allah Almighty says: ﴿And do not invalidate your deeds﴾ (Quran 47:33). If she fasted without your permission, then she has erred, and there are two opinions regarding the permissibility of forcing her to break her fast. She must repent and make up that day without expiation, because expiation is only obligatory for breaking the fast in Ramadan.