Was this ever fixed for you? I am having the same issue in 2025. Just started a new payroll item that is an addition to paychecks. QB paystubs are correct. Workforce website & app are deducting the addition causing an incorrect net pay (on the app view) and YTD net pay (on the workforce view). Downloaded paystubs from workforce & app are correct but you have to manually do math since there are no totals.
