Let me help share information about the things you need to consider which will affect the calculation of your employee federal taxes.
When you enter W4 employee details in the payroll system, federal taxes are calculated not with a fixed rate. But consider taking note of the following information and making sure they are accurate for the correct calculation of your employee's taxes:
The employee tax withheld depends on how the payroll is set up. Since you've already checked, I'd suggest reaching out to our Customer Care Team using our QuickBooks Online Sample Account. They'll be able to perform a screen share and identify the root cause and create an investigation if necessary.
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You can always run payroll reports to review the wages, information, and any more by customizing. Click the Save customization button, so it'll be saved on your Custom reports tab. It helps you quickly run the report in the future. To learn more about this process, visit this article: Memorize reports in QuickBooks Online.
Additionally, you can visit this article on how to check the employee's annual wage base limits in your account.