I'd be glad to help check why federal withholding is not taken out of your employees' paychecks.
QuickBooks calculates the federal withholding based on these factors:
Number of allowances/dependents
One reason why federal withholding is not deducting correctly, is when the employees' profile are not set up correctly. It's possible that your employees' payroll taxes weren't set up in their profiles. To check this further:
Click on Workers at the left pane.
In the Employees tab, find and click your employees' name one at a time.
Click the Edit employee button.
In the Pay tab, click the Edit icon (pencil image) in the What are [employee's name] withholdings?.
Check the tax set up of your employees and correct them.
If the taxes are set up correctly on your employees' profile, I recommend contacting our Support Team to check and verify this further securely. For the support's contact information, you may check it here: Contact the QuickBooks Online Customer Support team.
On the other hand, you can also check the IRS 2019 Publication 15 to verify the exact computation of the withholding amount.
Please feel free to add a post/comment below if you have any other questions about federal withholding. I'll be always here to help you!