Minnesota requires that taxable income and tax liability be calculated this way for part-year residents and nonresidents. There's no need to make any changes.
The state starts with total federal income and calculates tax liability based on that income. Then an income tax percentage is applied to prorate the tax liability. The income tax percentage is calculated as MN income/total income. In your case, your income tax percentage is 0%. Therefore, you don't have a tax liability and instead will be refunded all of your withheld tax.
