This is the way that the NY tax is calculated. The return will use all of your income, and then prorate the tax. While it's a strange way to calculate it, the final result is a lower tax than if the income had been earned in NY.
If your tax is very high, you may not have yet allocated the wage income in the New York interview. If you're not sure, the best way to reset the NY return is to delete both NY and Michigan returns and then add them back, starting with New York to get the proper result.
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