Really cool game! your waves are out of sync though, the goal waveform (and the way the waves you have interact) changes as time passes, I was going to add two screenshots I took to show this, but for some reason the add image thing wouldn't load, but if you wait a bit in a level it's easy to see the change. it makes it harder to visualize when your goal is moving. Also, if you plan to keep working on this, it might be a good idea to add the option to see the waves standing still, the movement makes it a bit harder to visualize how they add and multiply, and maybe always have the zero line, to more easily identify when the wave is negative and when it is positive.
It's also cool that this concept allows you to think in two different ways to solve a puzzle, because you can also think about it as the intervals formed to solve it, which is what I did occasionally to bypass the phase desync problem, since the frequencies don't change so you hear the same result, though it's a bit hard, since you can have three waves at octave intervals, and in the result you hear a third, but it's because modulation changes how they relate differently than addition. It might be a good idea to exploit the possibility of solving the puzzles musically, by adding a way to visualize how frequencies interact, or teaching how they interact in terms of intervals, so there's two paths to solve each puzzle, by visualization or by hearing.
Is having a timer a good idea for a puzzle game? It's kind of stressful, specially if the game doesn't tell you what the timer is for, and it made me want to pause the game while I pondered the solution.