just the rhythmic guitar part was played during certain scenes.

What I meant was, (for example) in the film, did Dustin Hoffman say "Koo Koo K'Choo Mrs Robinson", or are those words only in the song? My impression was that the soundtrack and the film were kind of created at the same time (could be wrong about that), and perhaps the filmmaker and Simon/Garfunkel were trying to say something with that line. Just speculating.