You want to make sure your MS return only shows the Mississippi income. Make sure you indicated that both of you are non-residents.
Mississippi takes your total income and divides by your MS income, to figure a %. For example, if you earned a total income of 40K, and 10K was earned in MS, then 25% of your income would be taxable in Mississippi.
You should get a screen in the MS interview that shows 'Federal Income' (total for you both) and a place to enter 'Mississippi income' (where you would enter only MS amount).
Here's a copy of Mississippi Form for Non-Residents that may help you to check the calculations.
You may want to delete your states and go through the MS interview first. If the amount of MS tax withheld is correct on your W-2, you should reasonably 'break even' with MS, or get a small refund. However, if not enough MS tax was withheld by your employer for the MS income, you could still owe tax on this income to MS. However, you are correct that you should not owe just by including a 'non-MS' W-2.
Since we can't see your return in this forum, you can Contact TurboTax Support for help.
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