If the control totals are only out by the employee(s) that moved pay groups then manually write in the figures on the control report. You can stand over these figures as you know where the discrepancy is originating from.
This is likely down to the timing of the Pay Group change. Check for Items to consider when moving an employee's pay group.
Although this article refers specifically to the controls totals not balancing, this issue extends to the final control reports in reference to when you have the employee moving pay group.
We advise that it is okay to proceed and a manual intervention is not required. Simply noting the change is sufficient in an audit perspective.