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TurboTax is likely trying to save you some tax dollars. Please look at line 2 on the IA 1040. See where it says, "Married filing a joint return. (Two-income families may benefit by using status 3 or 4.)"
I have seen other states do this, but TurboTax asked you if you wanted to make the change. Here, apparently, it was so obvious that you would benefit that TurboTax chose option 3 (in my test).
So, likely, there is not a problem.
Your Federal may be MFJ..
BUT
......the selection for the IA tax return has selected to be selected again, right at the very start of the IA interview.
Go thru the IA interview again slowly from the very beginning. IA does allow you to do MFJ-Federal and MFS-IA, but it is not required, and I wouldn't normally mess with a MFS-IA set if I didn't have to.
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