Based on the facts you have mentioned, there is no defect in your title and there is no immediate or compulsory requirement for you to execute a fresh sale deed at this stage.
In Maharashtra, for flats sold by builders, a registered Agreement for Sale executed under the Maharashtra Ownership of Flats Act, along with full stamp duty and registration, is a valid and legally recognised conveyance of ownership rights.
Since your agreement to sale was registered, full stamp duty and registration charges were paid, possession was handed over, the society has been formed, conveyance of the land and building has been completed in favour of the society, and the share certificate has been issued to you, your ownership is complete and marketable.
The belief that a separate sale deed is compulsory is a common misconception. In builder-flat transactions in Maharashtra, the registered Agreement for Sale itself functions as the sale document, provided it is properly stamped and registered. A separate sale deed is not mandatory unless the agreement specifically states that a sale deed will be executed later, or the agreement was unregistered or inadequately stamped, which is not your case.
That is why it is normal and legally correct for all society members to hold only a registered agreement to sale.
You can technically execute a confirmatory deed or a deed of sale even now, but this is optional and not required by law. If you choose to do so, stamp duty and registration charges may again become payable depending on how the document is drafted, but no additional legal benefit is usually gained. There is no penalty for not executing a sale deed now, because the law does not mandate it where a registered agreement already exists.
At the time of future resale, you can sell the flat directly on the basis of your registered agreement to sale, share certificate, and society NOC. Buyers, banks, and registrars routinely accept this. You do not need to first execute a sale deed in your favour before selling the flat.
A sale deed would become necessary only if the agreement was unregistered, stamp duty was deficient, or title was never properly conveyed by the builder, none of which applies in your situation.
In simple terms, your ownership is already complete, no penalty applies, no compulsory sale deed is required now, no legal issue will arise at resale, and executing a sale deed at this stage is optional and usually unnecessary.