What should I do? My wife was issued 1099s with her SSN, but the business is an LLC taxed as an S-Corp.

If your wife is a shareholder of the S-Corp and the income reported on Forms 1099 belongs to the S-Corp, you can report that on the S-Corp Form 1120S return. As long as the 1099 income is reported on a tax return, you have satisfied the IRS requirements.

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