When you prepare a MFS (Married filing separate) return, you are required to enter the spouse name and social security number so IRS knows who you are filing separate from!!  That is standard on all tax returns that file MFS.  And if you prepared it correctly, it should say approved. And when the spouse goes to file their return, probably also MFS, they will report their spouse information on their return marked MFS.  And there will be no rejection message that the SSN of one of the people has already filed a return.

So I do not see any reason for concern!!  But you know what, you have your eyes open, noticed something unusual and then "phoned a friend" here in this forum!!  You did a great job!!