It's an issue with Godot on the web unfortunately, when you're dropping frames the audio starts clipping and crackling. Judging by the other comment, the lua integration must be doing some heavy work.

I found that if I remove the number lines or position the display straight on to an axis, that the crackling drops considerably.

Same for me, when the code is not correct, the music is much slower and very crackly. Once the code gives the correct solution, the music speeds up and the crackles go away.

Also agreed, very fun!