Have you purchased both flats ? If yes than single MC payable otherwise both owner's have to pay separately.

Since there are 2 separate agreement executed by builder for 2 flats society is justified in charging you for 2 flats 

even if there is one kitchen  ,one door Society can charge you separate maintenance 

If building plan shows only 1 3bhk flat, then despite there being two agreements, the society has to charge for only 1 flat and not separately for the 2 combined flats

File a case in the consumer court.

You challenge the maintenance bill before Cooperative Court at Ballard Pier Old Customs House ,under section 91 of MCS Act 1960 for exorbitant and excessive amounts over and above normal maintenance charges comparing to other members in the Society. 

Make Society, Chairman, Secretary and Treasurer as necessary parties in your disputes for excessive maintenance charge. 

1. if the sanctioned plan show only one flat and in reality it is one flat  as well which is further apparent from the existence of one kitchen then maintenance charge can not be obtained as two flats.

2. For this anomaly alone in most of the states under Apartment Ownership Act the maintenance charge is calculated on the area of flat and not the number.

3. If in your society the system is on number of flats then refuse to pay for more than one flat and the society can not take any lawful action for your refusal to pay as per their demand.

File a complaint in the RERA against the builder. 

1. IF the BMC sanctioned plans show only one Flat with one Flat number, THEN the Society is entitled to issue you only one share certificate & one voting right, only one maintenance bill, without any further legal exceptions.  You can also check this with the BMC  Assessment Dept., (property tax bills) as to how your Flat is assessed.

http://chshelpforum.com/service-charges-of-chs

2. Builder sometimes makes two agreements for one flat, for income tax & other tax purposes. But this is a privity of contract between Builder and Flat Owner and the Society has nothing to do with it.

3. You have an positive option to file a grievance petition against the Builder /Developer, in the local Consumer Court, for their illegal trade practice, negligence, deficiency, harassment, intimidation, cheating etc.... with proper documentary evidences and you can claim damages /compensation & interest on your investment, and for your physical & mental trauma.

This is a two flat combined by the builder illegally.

If there are two registered sale deeds then it cannot be considered as a single unit.

Therefore you first take a legal opinion from a local lawyer, and also if you agree for paying the extra amount demanded by them then you can buy the flat or else you drop the purchase and buy  direct single unit flat.

You cannot get any case law for such illegal dealings.

- Since, the building plan is showing 3BHK, with one door , then it will considered as one unit and not two independent flats , and the society cannot charge maintenance for two units on the ground of two agreements. 

- Further, the most popular method to calculate the maintenance fee is , Area wise maintenance i.e. according to the area in terms of per square feet owned by each member.

- On refusal by the society to treat as one unit, you should lodge your complaint with the Deputy registrar.

-  You can also file your complaint with the Consumer court as well. 

If as per plan it is one flat then it will be single maintenance. Maintenance is divided as per member and no of flats divided by total expenses. 

How did he sell you a single flat while the agreements were 2? It means that either there were initially 2 flats but they were made into one or ghere has been sone changes in the plans. The maintenance amount cannot be arbitrarily charged. Send the society a notice and file a case with the registrar.

Dear sir,

The maintenance charges will be as per the society bye laws. You are suggested to confirm the same and then submit your objection in writing. 

If those are for two separate Units merged together, then the said merged Unit will be considered as two units for the purpose of claiming maintenance.

 You should file case before consumer forum against society and builder for charging double maintenance charges.