Pleased to have you here, @MEmerson2.

Thank you for dedicating time to search our Community for possible solutions. I'd be delighted to provide insights into the reasons behind the incorrect deduction of federal taxes in QuickBooks Desktop (QBDT).

Here are the possible reasons QuickBooks aren’t calculating federal taxes properly:

• Total annual salary exceeds the salary limit.
• The gross wages of the employees' last payroll are too low.

You can pull up Payroll Summary report or Payroll Detailed reports to check the calculation of one of the employee's paychecks to see if it matches QuickBooks. To help figure out the exact withholding amount, please go through the IRS 2018 Publication 15.

If the calculation is incorrect, you can create payroll liability adjustment. However, if it's correct let it be. 

Also, here are the lists of articles you can read more about paycheck calculation in QBDT:

• Payroll items on a paycheck are not calculating or are calculating incorrectly.
• QuickBooks Desktop calculates wages and/or payroll taxes incorrectly.

For future reference, we also have a variety of reports you can pull up in QuickBooks Online Payroll in case you need help checking up on your employees' data and other payroll-related concerns: Run payroll reports.

Reach out to me again if you have other payroll-related concerns or questions about QuickBooks. I'm always willing to assist you in making your business run smoothly. Have a wonderful day!