You will have to pay stamp duty with penalty decides bby Registrar.
Legal liability is not on society as the certificate they isuur ID about no dues of society charges.
Yor deal with the seller was not diligently done.
Before 2011 there were many sale in Mumbai and other parts took place without registration .the buders originally sold many flats without registration.
It is unfortunate that you purchased a flat which had no clear registered document.
Factually societies don't initiate to notify the members regarding non payment of stamp duty and registration unless they go for conveyànce certificate.
No point in taking criminal steps,so better to pay stamp duty for the chain documents which can be claimed from concerned sellers.
No cause of action arise against society and it will not come under consumer act.the non due certificate intents the duesbtowards the society.