QuickBooks calculates your Social Security (SS) and Medicare (MC) based on the rates mandated by the IRS. Let me provide more details about this and help you further.
The rates mandated by the IRS for your SS and MC are already fixed. There's no option in QuickBooks to change these rates.
You can pull up your Payroll Detail report. This way you can verify the tax miscalculations on your paychecks. You can pull up the report by clicking on Reports and looking for Payroll Detail on the search bar.