I would recommend you to check Calculation logic to identify the calculation errors.
Once you are in step 2 and have calculated the salary, click on Calculation Logic under Actions. You can cross check the calculated values and see how calculations are made.
If needed, make adjustments by deleting the calculated payroll for a specific employee and adjust days worked, extra payment, deductions or total TDS. Also make sure you have mentioned the correct values in all the salary heads of that employee’s salary structure.
If still you face any issues, Request Support by clicking the icon given in the application.