You need to have been ordinarily resident in the UK for 3 continuous years for reasons other than full time education. The people who offered you a place should have checked your status earlier. Problems arising from inefficiency in university administration departments are all too common. Unless you supplied them with incomplete information, the mistake is the universities fault. However, the universities only impose the rules for studentship funding, they do not make them and it is not their money. If your residency status does not qualify you for a grant there's nothing they can do about it. The only discretion they have got is to charge you 'home student' fees, which they have offered to do.
If you feel that your status does qualify you for research council funding and the university have made a mistake then write to the registrars office. Also contact the NPC (National Postgraduate Committee) who should be able to give you advice and support.