Thanks for playing and I'm happy to hear you enjoyed it so much! About the notes: Some ingredients do not have any effect (like water), that's why even if you have only one possible effect left, you might need to verify that it has any effect at all.
However, there is unfortunately a bug in the notes that doesn't consider secure knowledge (green tick) of all other ingredients you used. This could lead to an effect not being checked off even though you have all the required knowledge to do so. If I find the time later today, I'll provide a fix.