There is supposed to be a short transition window when playing a new sound to prevent the popping issue. Is it on the "Note names" lesson recap? Also if you don't mind sharing your version of iPhone/iPad, I'm concerned some older devices might have performance issues since the audio is synthesized in real time, maybe increasing the window could help.
As for the audio being completely broken and needing an app restart it actually happened to me a couple times during development but I was never able to understand how or why it occured and haven't seen it again since months so no fix in sight...