This issue happens because the employee has control over the company.
You may check it under Personnel, Add/Update Employees, Setting tab, PCB Setting.
Based on LHDN, "THE ABOVE EXEMPTIONS ARE NOT APPLICABLE TO EMPLOYEES HAVING CONTROL OVER THE COMPANY, SOLE PROPRIETORS OR PARTNERS OF PARTNERSHIP BUSINESSES".
You may refer to: http://lampiran1.hasil.gov.my/pdf/pdfam/Notes_PartF_2.pdf
Payroll Setup & Maintenance: Missing 12-Month Figure Updates for Specific Employees
Figure for 2 employee didn't appear in 12 Months Figure Update (Tax Exempted Allowance)