The system calculates federal and state income taxes by following the IRS Publication (Circular E), Employer’s Tax Guide. To ensure there were no federal taxes on employees paycheck, let's check if their profile is set to Do No Withhold.
Here's how:
In the left menu, click Payroll.
Go to the Employees tab.
Select the name of the employee.
In the Employee details tab, tap the edit (pencil) icon beside Pay.
Click the pencil icon in question # 2 for what are your employee withholdings.
In the Federal filing status section, ensure that the Do not withhold (exempt) radio button is selected.