Thanks for the detailed criticism! It really helps to get honest feedback like this, and we're definitely aware that our game still needs some polish after our mad scramble to finish it in time.
I think your comment about potentially misunderstanding how the wave crossover mechanic works may be right, as the only purpose of crossing the waves is meant to be the 'clap' mechanic. The small purple notes can be caught by either wave regardless of colour; the waves don't need to be put together to catch them. That being said, it's pretty easy to see why you'd make that mistake, given the way the other small notes are colour-coded. We definitely should have made this more clear to the player by either choosing a different colour for the normal notes, or else having a message in the tutorial clarifying that the small purple notes ignore wave colour.