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That would be between your wife and her employer.  All we can tall you is if she received a 1099-MISC then she is self-employed in the eyes of the IRS and must pay the both the employees and employers share of the SE tax and income tax.    Since there is no tax withholding for self-employed persons, to avoid under payment penalties probably quarterly estimated tax payments should have been made.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**