Following queries / documents to be verified and obtained from the builder:

Title Deeds: All documents of the title relating to the property which are in the sellers' possession or power. Clear title deeds held in the name of the builder / sole owner.
Builder should furnish a title clearance certificate, issued by a solicitor.

Permission to construct: Obtain Civil Authorities' approved construction plan and commencement certificate.
The architect should provide a certificate stating that the construction is taking place according to the rules of the Corporation.

Sale Agreement:
The builder must sign a proper sale agreement with you .
The sale agreement must have all the Annexures stated in Section 4 of the Maharashtra Ownership Flat Act, they include title certificate, property card (that indicates who owns the property), commencement certificate and sanctioned plans.
Include a 'specific performance clause' in the agreement.
There will be a schedule of payments.

Registration: The agreement must be duly registered ideally on the same day.

Occupation Certificate: After completion of construction, the builder obtains a building use permission or occupancy certificate from the civic authorities if the construction has been as per plan.

Possession: When you are taking possession, the builder will give a standard letter stating that you have verified the premises and found everything in order.
Actual facilities should match those promised in the brochure.