If the builder has provided partial OC and also registered the property to your name and delivered possession, then it becomes your duty to follow it up with the bank and the builder about the dues and the completion of formalities with the bank with reference to the deposit of title deeds.
You cannot blame others for your failure to ensure the follow up of the procedures.
The builder would claim rights to charge the interest as penalty for the delayed payment, you have no answer.
the bank is just a lender.
The bank is not interested in what problems you face.
It will follow the banking rules and regulations in this regard.
If you commit default in loan repayment then the bank will take action as per law for recovery.
The builder will remain silent until you go and ask him about the other pending issues.
If the builder was reluctant to answer to your queries regarding the pending works and provision of amenities, you should have taken legal action against the builder by dragging him to consumer forum
You are waking up on all such issues only when the builder is demanding the penalty, otherwise you would not have taken care of this even now.
Even now, citing all the lacuna on the part of builder you issue a legal notice demanding him to make alright all the deficiencies including issue of OC and inform him that he is not eligible for any penalty because he has not made the demand notice to the bank when it was due, the current demand notice is not legally maintainable as he had not intimated about this earlier, hence his intentions are malafide to grab your money.
You somehow have to create grounds to tackle the builder and get the penalty waived or reduced to some extent.