About gotra system

Get a Registered marriage or in Arya Samaj.  Those things are not material in those cases.  In South India these marriages are common, as daughter after marriage belongs to another gotra as she will be taking the gotra of her husband.  Then brother and married sister's gotra are different.  Scientifically, some advise against such marriages within relatives.  When there is no direct relationship in between the couple's families,  there may be several combinations later in several marriages, belonging to same gotra may not have any such defective genes.