My basic problem with this story is that it really doesn't hold up to scrutiny in terms of the world building. The author claims that the characters are sent into training for the "rank and file" instead of the "elite" but makes them superior in skill to their "elite" peers. He also contradicts himself on how his rank and file ninjas rise in the ranks, stating in his author notes that it's rare and then, in story, mentioning that several of them were up for promotion.
In this sort of story, you can contradict canon, if you do it in a manner that is thoughtful and planned out. Many great stories are based on that very process. But you can't contradict yourself, unless you're extremely good and have a plan that will blow your readers away. This is not an example of that. The conflicts show a failure to really think about how the story's plot and the author's world building interacted.