And the reject explanation says?

Spouse filed her return separate with his social on her return.

Instead of her SSN?  What exactly did she do?  And have you actually seen it?

Her return has her social as PRIMARY and his as spouse

His return has his social as Primary and her as spouse

I did see her return

rejection notice the primary ssn in the return header must not be the same as the spouse ssn on another return with filing status mfs.

the t/p social has been listed as the spouse's ssn on another tax return filed as mfs

I am going to assume that you have double checked that the correct Social Security number is properly tied to the correct spouse.  I remember a few years back that I had issues with filing a MFS return after the spouse had already filed but I don't recall what I had to do to get things to fly.  Unfortunately, I think you might want to try calling support.

"rejection notice the primary ssn in the return header must not be the same as the spouse ssn on another return with filing status mfs."

Are you sure it says that? What else would be the primary SSN on a tax return when their spouse filed MFS and list your client's name and SSN as spouse?

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?  

@kathykalosky1 Thank you for being here on the Community! If you haven't already we would direct you to ProSeries Support to help with this.