Before tax season, the IRS gets a database from the Social Security Administration (SSA) of taxpayer names and social security numbers.
Sometimes, what you think is your last name isn't what the SSA thinks is your last name. This often happens with Hispanic taxpayers who have first name/father's last name/mother's last name as their formal name, but use their father's last name as their last name in English. The SSA is likely to consider the mother's last name as the last name, since it is, well, last.
Call the SSA and confirm that your spouse's name and SSN are correct. Consider that your spouse's name might need to be re-arranged to conform with the SSA's understanding of the name. If so, you can re-efile as if for the first time.
And if all else fails, you can print and mail your return, because this bypasses the e-file checking of name and SSN.
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