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When you encounter the special calculation situation pop-up, this doesn't always mean an incorrect calculation. It's QuickBooks working as designed. These are the reasons why you encounter it:
If the gross wage is too high/exceeds the limit, Federal and State income taxes (FIT and SIT) will not automatically calculate. When this happens, first, you'll have to check the employee's wage in the paycheck. Verify if it's correct by checking the Earnings section of the paycheck. If it's correct, you'll have to calculate the FIT and SIT manually and enter it in the paycheck details.
Though, if the wage is incorrect, you'll have to adjust/change the employee's salary/hourly rate. Here's how:
If the employee's wage is too low, it might be the correct calculation of FIT and SIT is zero. You can refer to the Publication 15, Circular E, Employer's Tax Guide to check the accuracy of the calculation.
I've got you an article for future reference: How QuickBooks calculates payroll taxes.
If you need more help, you can always leave a comment below.