Please follow the steps below to resolve the issues:
Go to the Payroll module and click Pay Records.
Select Year and Period.
Find the Employee, and take note of the details first before you recalculate it.
Unlock the pay record for the affected employee and click Recalculate.
Click Yes to Recalculate selected records.
Click No to 'Do you want to overwrite SSS/PHIC/HDMF/ECOLA/Taxation values?'.