The film ends with a log entry: "... and we star trek into darkness." and then the title is displayed. Similar to Nolan's Batman films, where the title is actually a description of the state at the END of the film, and not a description of the film as a whole.
Batman Begins at the end of the first film's story. He turns into The Dark Knight after Dent died. And The Dark Knight Rises at the end of the third film.