Internal Policy on Timekeeping and Attendance
There should be an existing internal policy pertaining to timekeeping and attendance, particularly regarding the filing of Official Business (OB) or Leave forms. If, at present, you don't have any written policy on this, then I don't think you can deduct from your employee's salary. If the employee applies for OB/Leave at a later date and that application is approved by the supervisor, then that application is already authorized or accepted; hence, a refund is in order. You can hold the supervisor liable since he/she approved the late application.
Legally, a deduction may be authorized if the employee is a daily/hourly paid worker.