If a film ( or play, or book or TV series) is set in a certain place, it means that this is where the action of the story takes place. When someone writes a story or makes a film, it is set in a certain place and a certain time - for example, 'Outlander is set in 18th-century Scotland'.
The film is set in New York =
The film tells a story about something happening in New York. We don't know where it is being made (it could be shot in a studio in Hollywood or Bombay)
The film is being made in New York =
The film company are shooting the film in New York. We don't know where the action is set (it could be a story about anywhere in the world, shot in a studio in New York).