If you have added extra payment for an employee, then you can remove it before finalizing payroll.
In step 2 of payroll processing, select the employee by clicking on the checkbox corresponding to their name and click on Adjust data.
Click on the value and modify it. You can make it zero if required and leave a note in Narration.
Remember, this note might show up in the payslip in case you are adjusting the data after payroll finalization.