Author's Saving Throw: After Season One was written, Lauren Faust made several Word of God statements that Jossed almost everything Vinyl Scratch accused Celestia of in her interview, thereby making Vinyl look like an utter bitch making false accusations about one of the rulers of Equestria. Season Two, Episode Three has Luna tear Vinyl Scratch apart for making false accusations about one of the rulers of Equestria. Readers had mixed opinions on this.
Season 2 Episode 4 has Luna backpedaling a bit herself.
Fanon Discontinuity: Many fans like to pretend that Season 2 never happened, which is made easier by the original Audio Adaptation ending shortly before the point when the 2nd Season got controversial.
Fridge Logic: The story casts Princess Luna in a very positive light, but Octavia freely calls Vinyl a lunatic. Considering the root word and original meaning of that word, it should be very taboo in Equestria.
Harsher in Hindsight: "Ponyville Confidential" had many tropers feeling bad when a town was shunning three small fillies for a single day when their insensitivity caused problems. Now imagine pretty much the whole of Equestria openly wanting their deaths and attacking them wherever they go, for months on end. That's Blueblood, except without two additional ponies to share his pain with (at least at first).
Then again, it's difficult to feel bad for someone who's heavily implied to use unpaid children for labor, and would use the body of another pony to put out a fire.
Tear Jerker: The end of season 2, episode 2. Blueblood tries to ask Trixie out, but winds up accidentally offending her, driving her to storm out of the station. A lot of the time, he's a total jerk, but here he's really trying to be nice. When it fails, he goes into such deep sadness and self-loathing that he spends the whole night getting drunk and repeatedly puts himself down over the next few days.