To update the employee's time record navigate to Manager > Reports.
Select Labor > Payroll Details > Select the start and end dates that the employee did not get paid for > Click Generate.
You will see the TR (Time Record) the employee is referring to as it will state "Auto Clock Out" next to it and will have a total hours of 0. It will however show the estimated time that the employee clocked in for their shift.
Click on the TR to edit it.
The record will popup. Edit the end time; which is the time the employee ended their shift. If they were a driver; edit their dispatch hours (how long they spent delivering orders) and any tips that they may have received. Click "Update" when you are finished.
The record will be updated and indicate the correct hours/pay for that shift, and that the record was edited.