What is the rejection code?  IND-508 or IND-511?  This is what a TurboTax reference page says about 508:

"This error often happens if your spouse has already filed your joint return, or if they filed their own return as Head of Household and put you down as their spouse."

What is the filing status on the spouse's return?  Why is this couple filing separately?  Do they live together?  Are they in a community-property state?  Do they have children?  Did she claim the children?