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You need to request your IRS forms or account transcripts for that year. Does the notice say the distribution code for the 1099R? I am assuming it is 1099R. When you look at the notice, there should be a section a table where IRS states what form is it, how much was reported to IRS and how much you claimed on your return. Does the description has a distribution code? Did you wife had a loan from her 401K maybe?
Here's how to get your online transcript. It is a line by line version of all forms reported to IRS from third parties under your our your spouse's social security number.
Once you get the transcript, you will have to contact the issuer directly. Maybe there was a social security number mismatch. The issuer will need you to issue corrected 1099R that you will use to respond to the IRS letter.
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