Michigan and Indiana do have a reciprocal agreement for state tax. As Michigan resident that works in a reciprocal state, you can fill out Indiana's exemption form - WH-47 and give it to your employer if you don't want them to withhold Indiana taxes. If you haven't done that, you will have to file a Michigan state tax return and an Indiana non-resident tax return, if you want a refund of the Indiana tax withheld. If you had not Indiana tax withheld, you don't need to file an Indiana tax return.
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