Within days of the game’s launch, players found a game-breaking Paper Mario: The Origami King glitch. Now completionists have picked up on a second glitch involving Black Shy Guy. While this one doesn’t break the game, it does prevent you from getting 100% completion. This can be an infuriating thing to see.
— Sergio Montenegro (@Sergiomonty) August 2, 2020
This problem stems from one point in the game when you’re tasked with taking out two Black Shy Guys. Since this is a story segment, these enemies will only appear once. As long as you manage to defeat one with Mario, the Black Shy Guy will then be added to your record of defeated enemies, pushing you one step closer to 100% completion. However, if your partner for this quest, Captain T.ode, is the one to land the final blow on those Black Shy Guys, they won’t be added to your enemy compendium. As a result, 100% completion is out of your grasp unless you restart.
While Nintendo hasn’t said that it’s aware of this Paper Mario: The Origami King glitch, it is releasing a patch to fix the previously discovered game-breaking one. Hopefully the developers take note of this oversight as well and fix them both soon enough.