When you enter each business separately, the income tax is computed and also the SE tax. There is a tax bracket difference between just his income and your or his and joint.
Self-Employment tax (Scheduled SE) is automatically generated if a person has $400 or more of net profit from self-employment. You pay 15.3% SE tax on 92.35% of your Net Profit greater than $400. The 15.3% self employed SE Tax is to pay both the employer part and employee part of Social Security and Medicare.
By the time you enter both businesses and compute SE tax plus federal tax vs what you have paid in, you see the results. There have to be some other credits coming into play here as well. Gross income vs net income can be a big difference. You may have EIC, retirement, or other, coming into play
As an owner, you are not an employee. Without seeing your return, I can't be of any more help. I wish I was sitting there with you!
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