Make sure that you entered all of the boxes from your W-2. As long as you entered all the numbers correctly, you can rest assured that TurboTax did not double-tax your income. Tax is applied to all of your income. However, if you entered the amount from Box 2 of your W-2, that amount is credited to your tax liability.
You probably notice the extra taxes generated from your spouse's self-employment income. When you are self-employed, you must pay both the employer and the employee portions of social security and medicare tax. This is the Self-Employment Tax and it is 15.3% on top of the ordinary income tax that is due. You should have a Schedule SE in your tax return where you can review this. The link has more information as well.
Tax Tips for the Self-Employed The good news is he can also use Schedule C to list his deductible expenses for things such as advertising, insurance, employee wages, and equipment he purchased to do your work. Expenses will lower his net income and therefore his SE tax.
If he made estimated tax payments, you can enter those by following the instructions here.
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