Clarification...When you say My return versus his return are you talking about Schedule C's? Or did you file as Married Filing Separately?
You said he received the deduction, but your income is included. That should not be the case. Your self-employment income should not be on his Schedule C. Did you create 2 separate businesses by selecting add a business and then making sure each person is assigned as the correct owner of the business?
If you are using TurboTax Desktop, form 7206 is not supported for e-file so you will need to print and mail your return.
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