Bizarro Episode: The original version of chapter 18 — covering the formation of a unified Equestrian government after the Winter War, it suddenly runs into a tangent about how awesome Puddinghead's parties were, then describes a scene where Hurricane and Slendermare fought over who's sexiest, and then there was an orgy... and then Twilight Sparkle wakes up at her desk, where she fell asleep working on the text. This was an April Fool's Day joke chapter, and it was later moved to Brief History: Side Stories and replaced with a proper chapter.
Fridge Horror: In spite of what the narration says, it is strongly suspected that Mareinus and Sullamander were lovers before the latter's appointment as Second-in-Command, and that Mareinus was a pedophile with a filly fixation. So what does that mean about how far back their relationship goes?
Princess Platinum's final moments, wherein she convinces herself both that her father and Star-Swirl would be disappointed in her and that she'd be facing eternal damnation for the Necessarily Evil acts she performed for the greater good. Also, Velvet Hooves' and Clover's emotional breakdowns in reaction to her death.
There's also Platinum admitting to herself that the reason she's never let herself return Velvet Hooves' love for her is the fact that, with her Special Talent being literally a Manipulative Bitch, she can never be sure that she didn't subconsciously make him love her.
At one point, a letter from Smart Cookie mentions that of her seven children, only four of them survived to adulthood.
