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.
Twilight: Thanks for helping me organize the library. It's good to know that I have friends to count on when plotting murder.
Rarity's brainwashing spell comes with everyone under it getting giant googly eyes. It's funnier than it sounds.
Fridge Logic: Nightmare Moon taught Rarity the mass brainwashing spell. What stopped her from using that to stand up against Celestia one thousand years ago?
Moral Event Horizon: Celestia gets at least two in this series. The first one is leaving Twilight's parents polymorphed into the forms Twilight accidentally changed them into even though she knew how to undo it (for reasons why this is such, read the definition for And I Must Scream). The second one would have to be killing Luna despite her begging.
What makes the first one worse is the fact that Celestia told Twilight that the spell was irreversible, when both of them knew that not only could it be cured, but it could be cured easily.
What Pinkie did to her family and to Gilda may fall under Kick The Son Of A Mule for some, but how she casually reveals she murdered three fillies over a minor misunderstanding and laughs about it with her friends shows the extent of her twistedness. Particularly since the audience is made aware that two of those fillies were the little sisters of two of her friends...