1) Can we raise this as a legal concern against the buider?
Yes, you can raise this issue with the builder by first communicating to him in writing to him and get his acknowledgment of having received the communication, get his reply, dont worry even if he is not replying, secure the evidence and issue him a legal notice demanding the 50% share of land in the ground floor as was agreed and reduced to writing as conditions in the JDA quoting the relevant clause in the said terms and conditions of the JDA;
2) Builder was also un-fair in allotting the car parking slot. (MAIN Concern) For all the 3 flats owned by builder; the cars can be taken out with-out disturbing other cars. But for the 2 flats owned by the land-owners; he has allotted the car parking in such a way that: we need to move out one car; to take another car. We are really dis-appointed with this. Can this be raised as 'Unfair allocation of Slit area'.
The builder cannot take away the car parking area as per his convenience, it can be common and not one suiting his benefits alone, in the same legal notice you can demand the fair distribution of the car parking space properly to all the flat owners of the complex.
The legal notice may not invoke response or proper response hence you may subsequently approach either consumer forum for deficiency of service citing breach of T & C of the JDA and also you may approach civil court for property relief by filing a suit for mandatory injunction.