there is a bug on at least the web version but sometimes the notes just disappear (idk if that is intentional or a bug)
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Yes it's a glitch caused by too much lag. The next update will have a re-write of the note spawning code that should fix that. Until then there's a few things you can do that should help prevent it. Make sure graphics acceleration is on in your browser's settings. If you're using Firefox, try a Chrome (or another Chromium based browser), as Firefox has issues with Godot web games unfortunately. If that doesn't fix it, the downloadable version should have better performance, making this less likely.