First of all he couldn’t file Joint and Head of Household. It’s either one or the other. If he filed Head of Household you would need to file as Married filing Separate. So if your return rejected he must have filed Joint. Did he have all your info and income for the Joint return?
I would ask the IRS what they did with your payment. Did they apply it to the Joint return? How did you pay the $650? Did it actually come out of your bank account or credit card? If your return rejected then maybe the payment did not go through.
