As an inversion, Naruto giving plot armor to Kakuzu so that when he's hit with Rasenshuriken, essentially an explosive tornado of microscopic blades, it somehow only damages half of his vital organs rather than just turning him into goo outright. He only survives that attack so the story can say Naruto didn't kill him, it was Kakashi who does it by walking in after the fact and executing him.

Also Pain, one of the most dangerous characters in the world at the time, failing to inflict a fatal wound on Hinata just so the story doesn't have to deal with fans thinking she was actually dead for the 2 chapters before the whole village gets revived anyway.