Because you are a resident of Alabama you are taxed on 100% of the income that you earn in any state while you're a resident. However, Alabama also will give you a credit for taxes paid to another state and you can deduct that amount from the taxes owed to Alabama. The TurboTax system should have entered the taxes paid to New York into your Alabama return as a credit amount after you did the non-resident New York return. This credit avoids the double taxation but you have to have the income there in Alabama to qualify for it.
So you need to fix your income back to where it belongs and make sure that you are getting the credit for taxes paid to other states.
@DoctorJJ
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