Have a similar case with my purchase.

Get a chronological of event from both the loan lawyer and SPA lawyer (I believe SPA lawyer is also your lawyer, buyer lawyer?)
What about the seller lawyer?

Penalty fee is charged by who, usually it is charge by seller lawyer, please know whose lawyer represent who and the penalty is paid to who.

Read your SPA and load agreement to know more.
Usually, delay is delay, they don't care if land office issue or lawyer issue. Somebody is going to bare the mistake. If it is the lawyer that delay the submission or give error information, then you can ask the lawyer to bare the cost... but in order to do so, you must have evidence, so the chronology is important. If the lawyer submit late, submit wrong info, then they must bare the price

I suggest you pay the penalty first... but withhold the lawyer fee, or lawyer commission. Besides lawyer fee usually pay when transaction is completed. Once you have solid evidence, then deduct it from the lawyer fee

The question here is the penalty is paid to who? The seller or the bank that disburse your loan?
If it is paid to seller, it should be SPA lawyer collecting on behalf of the seller. If it is the bank, then yes, it is paid to loan lawyer.

Talk directly to them and see if they are willing to reduce the penalty if it is really the land office's fault.
This loan lawyer is appointed by the bank or you get yourself? Usually if it is appointed by bank, it is quite efficient.

As you already paid loan lawyer fee in full, I guess unlikely the loan lawyer will do much for you because money already in their hand.
Never pay in full, especially when you start doing renovation... think positive, pay for tuition fee to learn a lesson

By the way, if you are still want to give it a fight. Can complaint to Malaysia bar council
http://www.malaysianbar.org.my/contact/complaints/