Hello there, Central Lutheran.
Just like the previous responses of my colleagues, QBO will calculate the federal withholding taxes as long as the employee meets the taxable wage base and is set up correct. You can use this link for reference: 0.00 or no income tax withheld from paycheck.
If the same thing happens, I'd recommend reporting this to our Payroll Support Team. They can pull up your account and further review your data.
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