I noticed that too. I'm not sure if there's a better way to do it or not; as a piano player myself, it might seem more intuitive to me to have a visual indicator at each beat in the measure, and then just highlight each note (via color or something) as it's played. I think the reason it seems off is because it's so irregular, even though it does match with the music itself.

Kudos though, Etude looks great.