Hello there, @TLynn.
The possible reason why Social Security and Medicare calculated double is that QuickBooks perform an auto-correction to the paycheck you've deleted. To get this fixed, let's run the Payroll Summary report to verify the taxes if it needs to be adjusted.
Here's how:
- Go to the Reports menu, then select Employees & Payroll and choose Payroll Summary.
- In the Dates drop-down, select This Calendar Year.
- Then, manually multiply the YTD wage base to your employee's rate for Social Security and Medicare. And compare it to the amount on the report.
If the amount you've calculated manually is equal to the amount on the report, it means that QuickBooks made an auto-correction to the paycheck.
However, if it has a difference, you'll have to make a payroll liability adjustment. For more guidance, feel free to check out this article: Adjust payroll liabilities in QuickBooks Desktop.
Also, just in case your payroll items on paychecks aren't calculating, here's an article you can read for the detailed steps and information to fix it: Payroll items on paychecks are not calculating or are calculating incorrectly.
Please feel free to visit our Community forums again if you have additional questions about this. I'll be around here to help. Have a great day ahead.
