I prepared a bonus check for one employee on 12/28, the payment was on the same day as normal payroll. When I prepared the check the system withheld only the employee part of Social Security and were no suppose because he reach the limit of SS withholding. Then did the contribution to the IRS. Now I'm trying to submit through e-file the 941 for the last quarter of 2018 and QB is not letting me do it because I have an over-payment. I don't know what to do. I'm requesting a refund from the IRS to reimburse the employee.