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.
YMMV: Magical Pony Lyrical Twilight
Complete Monster: Sombra. He was once known as Lord Somber, and used smooth talking and charm to woo Princess Aria, who was the princess of the Crystal Empire and Luna's granddaughter. After he married her, he used love poison and dark magic to control her, killed her father, forced the crystal ponies to become his slaves and turned the Empire into the nightmarish wasteland seen in the show proper. Princess Luna became very angrywhen shesaw this.
Nachtwal. Yes, it's a broken defense program, but that doesn't exactly explain why Cadence sensed it was full of malice and hatred. Or the way it "listened" to Trixie. Or how it almost seems to be mocking the heroes.
Hilarious in Hindsight: A's began before Friendship is Magic's Japanese dub was announced. Shamal now shares a voice actor with Trixie. Particularly hilarious when they're both talking to Fancy Pants
The TSAB High Council. As of the end of A's chapter 12, they are giving Gil Graham two days to obtain the Book of Darkness. If he fails, they have implied that they will make something happen to Equestria. And if he refuses, they imply that something equally bad will befall someone Graham cares about. And when he finally caves in and does do what they want by freezing Trixie and the Book (for a few minutes), they proceed to A) forcibly assume control of the Arthra (including holding Lindy hostage), and B) decide to go ahead with their contingency plan - obliterating Canterlot from orbit - anyway.
Nachtwal killing the Wolkenritter. Even moreso than in canon because the canonical one was more misguided/corrupted than the openly hateful, omnicidal one here.
The Woobie: Fate in the first part, as per canon. Trixie in A's.