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After you file
If you did file schedule A and itemized, but the IRS has disallowed most of those itemized deductions, you will have to wait until you get their letter of explanation. I can’t think of any reason in the tax code that would allow them to automatically disallow your itemized deductions without performing an audit. If your spouse had filed and used the standard deduction, the fact that you itemized would have forced your spouse to itemize, not the other way around.
Did you print and mail your tax return? Maybe the data entry operator who punched in your numbers lost the page with schedule A printed on it, so they could only give you credit for your income taxes and not the other items.
You should have the opportunity of filing an amended tax return to correct the situation. You may have a 30 day deadline once you receive the letter, make sure to read the letter carefully. You can also contact the office of Taxpayer Advocate.