Does she actually earn the money in Michigan, or does she work in Florida for a Michigan company? Because if she isn't physically present in Michigan to work, the employer shouldn't be withholding state tax for her.
If that's the case, you should file a nonresident return and indicate that none of the wages were earned in Michigan.
Either way, Michigan requires that if you file a joint return for your federal taxes, you must file a joint return for Michigan. You would file as nonresidents, and on the pages that follow, you'll indicate how much of each income is from Michigan.
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