Applejack was stated to be in a coma in PARTY.MOV, and the Reset Button goes to a point after the end of APPLE.MOV, so it's still valid so we can assume she only travelled spiritually to canon!Equestria - so how can she reappear physically in the hospital in SWAG.MOV when she didn't leave that way?
She was in a coma in the comic. She went to Equestria Prime sometime after Party.MOV when she woke up.
Rainbow Dash's cutie mark and attitude depict her as being a Butch Lesbian. Her Catch Phrase (which inspires the finale title) is "Swag". One memetic concept can connect the two: SWAG is joked about standing for Secretly We Are Gay.
Fluttershy is the only one of the Mane Six who has never once uttered a curse word. Not even after she snaps and turns into a chainsaw wielding, ax crazy psychopath. This is strange until you remember that out of all the members of the Mane Six that Max chose to avert Sir Swears-a-Lot it was Fluttershy. He kept an integral trait of Fluttershy in her parody character: her politeness.
I can't believe this took me the longest time to realize, but in PARTY.MOV, Pinkie at one point tells Twilight that she has a big horse face, to which she obviously replies that she doesn't, yet has one. I always thought of this as a cheap gag, but then I remembered, Pinkie Pie's sanity is heavily damaged. She's hallucinating from all her substance abuse, and that one moment with Twilight is a Through the Eyes of Madness moment, for as subtle as it is.