These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Twilight Sparkle is definitely considered to be this. Her goal of preserving the essence of Harmony may seem admirable, but her means of doing so show that she does it out of principle rather than altruism. She brutally tortures her friends using scientific procedures, Mind Rapes them into forgetting their former lives (sans Pinkie, who has her throat torn out to remove Laughter), steals the pure essence of the Elements, skins their dead bodies as book covers, and keeps insisting that it's for a greater good. The way she performs these procedures completely changes her victims Rainbow wants nothing more than to kill Twilight and partakes in Autocannibalism, Pinkie can't speak, Rarity is emotionless with her jaw partially shattered, Applejack can't tell what's real and what's not, and Fluttershy is a rage-filled bloodthirsty maniac, with all of them trapped in an Afterlife Antechamber. Not to mention, she murders Spike, Sweetie Belle, Lyra, Thunderlane, Blossomforth, and Carrot Top, just because they were in her way. And it gets even worse - she plans to ensure eternal Harmony everywhere by calculating the genetic signatures of all the Elements, murdering any life form in the multiverse that doesn't have the genetic components to be properly harmonious, and seems to have absolutely no regard for any life that she deems "disharmonious" or "tainted". Though she snaps whenever any pony suggests that she herself is truly the tainted one.
In the fic, Twilight's secret Mad Scientist Laboratory is reached by a hidden, downward spiraling staircase, and her magic's color begins to progressively darken as she goes deeper into her Sanity Slippage. Fast forward to the Season 3 premiere, and Twilight's magic changes from its normal magenta to black as she uses dark magic to find a hidden downward spiraling staircase.
Also, the second chapter of the fic more-or-less begins with Rainbow trapped in Twilight's lab, with a device on her head, asking to be let go, and Twilight refusing. Fast forward to Double Rainboom...