The main instance where your tax due increases as your income decreases is when you have an earned income credit. Within certain income ranges, your earned income credit, which decreases your tax, can decrease as your income decreases, resulting in an increase in your tax due.
That is why the IRS requires you to enter all expenses and deductions applicable to your rental property.
The QBI deduction is a deduction from your taxable income, but it does not factor into your earned income credit, so I don't think that is negatively affecting your tax.
It is also remotely possible that you are not reading the refund meter properly. If the meter shows a tax due, then you reduce your income, the tax due may decrease and that can sometimes be misinterpreted to be a reduction in your refund.
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