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QuickBooks calculates your payroll taxes on the year-to-date amount. This is based on the payroll data and transactions you've entered. Here's more information on how QuickBooks calculates payroll taxes.
To make sure that the payroll taxes are calculated correctly, you should have the most recent QuickBooks Desktop software release and Tax Table updates before creating any new paychecks.
Then, check if the tax rates are correct for each payroll item by running Payroll Detail Review.
To run this report:
If there's any discrepancy, use a liability adjustment to correct employees’ data. For detailed instructions, see this article:
Adjust payroll liabilities in QuickBooks Desktop.
I'm always here if you still have questions about payroll taxes. Have a wonderful day!