You filed an extension for each of them. You did not indicate their filing status on those extensions. Just go back to your proforma MFJ return and mark that it has a valid extension and file the MFJ return. Keep the extension acks for the two extensions you filed.

This may mean you will need to decide how many returns you need to pay for, either use one of the two single extension files, or create the MFJ that you may not have yet paid for.