TS, your issue might be this 1? check with your HR.
its better to calculate how much u need to pay for ur income tax
total income tax = total amout of salary/side income etc - total amount exception from tax( ur epf, etc as u mentioned)

then from here,
ur PCB - tax income= tax refund ( unless ur PCB is deduction everymonth quite little, u should get negative, which is u need to topup)