Okey-doke, let's start with a little summary of just what happens at the end of the story, shall we? The nose is back on Kovalev's face, and Kovalev is back to his old life. Nothing much has changed for him besides the fact that he now has yet one more thing to feel all smug and self-satisfied about—the size of his nose. Meanwhile, the narrator grows totally disgusted with the nonsense that is the story and starts to rant about all the ludicrous plot holes.
So what are we to make of this? Well, to be honest, Shmoop's not really sure, and there's no way to know for sure. (We think that's kind of the point.) However, we'll throw out one idea: maybe the thing that really makes the narrator bonkers is the very fact that Kovalev totally doesn't change in any way despite having this big experience.
Think about it: usually stories follow a character from A to B. Someone starts out one way, has some kind of experience, and comes out of it a totally different way. Sometimes the journey is longer—A to B to C, for example. But it's not too common to see a character have a life-changing experience and then go about his business like nothing ever happened.
Not in "The Nose." Here, Kovalev seemingly learns nothing about himself or life or whatever from his two noseless weeks. That certainly seems like enough of a provocation to frustrate a narrator who's really been giving him the business during the whole story.