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We can't see your returns, so we can not be sure of what is happening. You seem to be saying that the state is increasing your Federal AGI by your SE income. That would seem to suggest either you are not reporting your SE income for Federal (but then the IRS would also adjust your taxes), or there is an issue when your federal AGI or income details are transferred to your state return. It might help if we knew the state. You should compare what's reported as AGI for Federal vs state. This is also a possibility that there is something else that could be causing this. For example, municipal interest reported in the federal section would not be in your Federal AGI but would be an add-back for state, but TurboTax should do this automatically if properly reported.
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