Chief Dominick J. Arena of the Edgartown police yesterday filed application for a complaint against Sen. Edward M. Kennedy for leaving the scene of an accident on Chappaquiddick, in which Miss Mary Jo Kopechne of Washington, D. C., was drowned. Senator Kennedy has admitted that he was the driver of the automobile that ran off the Dike Bridge and sank in Poucha Pond, with Miss Kopechne trapped inside.