Once you've verified that the set up is correct, I suggest checking the Payroll Tax and Wage Summary report.It shows detailed information about how QuickBooks calculates tax amounts on employee paychecks and the wage base limit for each employee's tax.
Let me guide how:
Go to the Reports tab located on the left pane.
Type Payroll Tax and Wage Summary in the search box and enter.
Customize the Date range and hit Run Report.
Click the Federal Income tax under Federal Taxes (940/941).