The problem lies with your W-2 since it lists wages taxable in Pennsylvania. The best resolution to this situation would be to get a corrected W-2 form that lists no state wages for Pennsylvania and then file an amended tax return. If you aren't able to do that, you can file an amended return for Pennsylvania and remove the wages for Pennsylvania on your W-2 entry and attach a note explaining why the income reported to Pennsylvania is not taxable there.
Another resolution would be to amend your Michigan return to reflect a credit for taxes paid to another state.
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