Quickbooks calculates UI tax due with the owner included, but MN UI says the owner isn't included in this. How do I resolve the calculation discrepancy on Quickbooks?

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In QuickBooks Online Payroll, some employees may be exempt from certain payroll taxes, when exempt from tax, an employee is not required to contribute to that specific tax. You can set up each employee as except from Social Security, Medicare, Unemployment, or other supplemental state taxes. However, you  may need to consult with a tax professional or financial advisor if you're not sure if an employee should be exempt from a certain taxes or not.

To change employee tax exemptions:

1. Select Workers at the left pane.
2. Select Employees.
3. Select the employee's name.
4. Under Employee Details, click on the pencil icon beside Pay.
5. Click on the pencil icon under the question What are (employee's name) withholdings?
6. Scroll down until you reach the Tax Exemptions section and click on the drop down arrow.
7. Select the taxes the employees are exempt from. Click Done.

For additional reference, you may check this article: Employee payroll tax exemptions.

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