Black Hole Sue: Ye gods, the deer warp everything to be around them. Of course, as they are obviously designed after Tolkienian High Elves, this is a rather difficult trap to avoid.
Still, they are actually the only part of the story considered to be bad by fans of the story.
Fridge Logic: Going to the princesses Celestia and Luna for assistance is never brought up as an option, and it's especially glaring when intervention on their part could resolve the entire plot quickly and without incident. Granted, from a narrative standpoint, it obviously would make for a much less exciting story; but this option is never addressed in-story, let alone given a justification for why it never comes up, or why it wouldn't work out. This glaring flaw is the story's one major shortcoming.
This flaw is explained in the last few chapters: Twilight refused to contact the Princesses because she thought that would look like she didn't have faith in her friends. Privately, Fluttershy fears that her judgement is being addled by the Horn Rot, and when she takes a turn for the worse, the only thing keeping them from immediately contacting Celestia is that Spike is out gathering herbs to help tend to her.
In the Epilogue, Princess Celestia finally learns why Twilight hasn't been writing to her, and is taken aback, even wishing that they had let her know so that she could at least ease Twilight's pain as best she could….
Les Yay: Rarity and Rainbow Dash in a couple of spots. There's Rainbow sucking on Rarity's horn in her sleep, Rarity tickling Rainbow when they were bathing, and this, from after Dash finally got the plural of 'Pegasus' right:
Rarity stopped hard. Her eyes widened. And in spite of the dire circumstances, she smiled enormously, lunging at Dash. “Oh, Dash, you did it! You did it! Nopony even needed to correct you! Why- why- I could just kiss you!”
She wrapped her front hooves around Dash's neck. The sky-blue Pegasus was taken aback for a moment, then grinned slyly. “Well, if you want to…”
Rarity drew back, an uncertain look on her face. Then she made a little noise and planted a soft kiss on Dash's forehead. “Done. Now don't say I never did it.”
In an obscure comic from a German magazine, most of Ponyville gets paralyzed. Rarity travels beyond Equestria's border to find a specific variety of barley to cure them, and she meets a kingdom of earth ponies there.
In the season 4 episode "Three's a Crowd", Twilight and Princess Cadance travel to the very edge of Equestria to find a rare flower, which is the fastest cure for a sick friend. Upon picking the flower, they're attacked by a giant worm.
The comic storyline "Root of the Problem" introduces deer into the franchise... and they're absolutely useless, only making things worse via their presence. Compare to the "WE ARE BETTER THAN YOU IN EVERY CONCEIVABLE WAY" depiction here.