A. Any university has competent to make their guidelines and rules and regulation within their limits. In my opinion, the allocation of seats based on percentage is not permissible because of eligibility should be considered at the time of admission of the Course not for hostel facility. Generally,the hostel facility would be considered for the accommodation to achieve and get the degree or qualification. In your case, read the rules and regulations of the University, if the university has not mentioned in anywhere, you can issue a legal notice to the Registrar of the University.
B. If no proper response for your notice, you can challenge the University act before the High Court by filing a writ petition and you have a good case due to it is not mentioned in the university prospectus. These claim of false affiliation with well known Universities in India as well as seat allocation based on wrong method without prior notice is liable to faces all the legal consequences before the Consumer Forum also under the deficiency in the Service.