Wow. I like the weird circumstances leading to me reporting this error. I geniunely thought the original secret item wasn't shown as collected on the map as part of the error, only to learn everything was fine (sorta). A suggestion of mine to make this less likely to happen is by making it clearer there are two secrets hidden (or showing which secrets were collected when selecting the stage, making it harder to guess how many there are before hunting for them). Or the hardcore way of not showing anything about secrets.
Anyway, thank you for looking into this and the tip, and sorry for wasting your time.