Sure, why not. As a tax payee, you have the rights to question and ask them to show you how they re-calculate your tax payment. They may not be able to do it over phone, you may try to lodge a case.

I would suggest to drop by the office where your file is located and get a queue number.

However, be prepared if it back-fires, i.e. you submitted wrong declaration or deductions, etc. and they turn the table saying you falsify without receipts/proof, and end up you have to pay fine (e.g. no books receipt, but still deduct 1k ... kantoi    ). But if you have nothing to hide and declared clearly, then you have nothing to be afraid.
Ask HR/Finance if they practise PCB for your salary range or not.
Ask your HR/Finance to help prepare the form to create an income tax account number.
You may/may not need to personally goto LHDN counter to open the account, depending on your company.