While Nintendo is still busy trying to fix the game-breaking glitch found in Paper Mario: The Origami King last month, another troublesome bug that hinders players’ progress has now surfaced. This glitch isn’t quite as severe as the previously reported one (which forces players to restart the game from scratch), though this new finding is certainly something for completionists to avoid at all costs.
As you navigate through the Temple of Shrooms, at some point you will enter a scripted battle against two Black Shy Guys. These enemies do not reappear in the game again after this encounter, and if Professor Toad delivers the final blow, this enemy type will not be added to your compendium, thus making it impossible for you to achieve 100% completion.
— Sergio Montenegro (@Sergiomonty) August 2, 2020
As long as you don’t let Professor Toad finish the battle, the compendium entry should fill in as normal. Hopefully, Nintendo takes note of this issue and can address it in its promised upcoming software update.