Did you select that he is a non-resident when you entered his name? If not, then you need to do so. If they do not have an SSN or ITIN and you choose to file Married Filing Separate ,you can enter spouses name and DOB and then on the next screen you can select "xxx is a non resident alien or dual status spouse" Make sure you put a check mark in the box that says My spouse is a Non-Resident alien in the My info section. When you get to the end and try to transmit the return, ignore the e-file errors regarding your NRA spouse and select transmit your return. If that does not work you will need to print and mail your return and write NRA (Non Resident Alien) in the space for her SSN.
If you are filing jointly, you will need to print and mail your return along with the W-7 which is an application for an ITIN and any other required documents to the address in the instructions