Continuity mistake: Fluttershy's neck disappears after she says, "I don't know if I can cheer enough to help her".
Continuity mistake: When Rarity levitates the stick to mark a spot where she detected the gems, she drops the stick right after a guard "threatens" her. Then, in the same scene, the stick has mysteriously disappeared.
A Canterlot Wedding - Part 1 - S2-E25
Continuity mistake: When the main six are running away from the changelings, Applejack's hat isn't there. In the next shot, it's back. That happens for the next two shots.
The Elements of Harmony (2) - S1-E2
Continuity mistake: When the ponies encounter the Manticore, it raises its paws and shows its undersides and Fluttershy notices something, even though nothing was there. Then when they stop attacking the Manticore, it shows its paw to Fluttershy to reveal a thorn, but the thorn wasn't there earlier. (00:05:25 - 00:06:20)
Continuity mistake: When the characters reach the clouds and Rarity shows her wings, Applejack is wearing a helmet hat. But later on she has only a regular hat.
Continuity mistake: At the end of the episode, Fluttershy reveals that she still has a fang left over from when she was a bat pony. This wasn't carried over, and her teeth have been normal since.
Continuity mistake: In Pinkie Pie's Smile Song, at one point, there is a magenta pony with a purple mane. To her right are a yellow pony and a violet pony. To her left, there are a blue pony and a turquoise pony. In the next shot, the yellow pony and violet pony are on the wrong side of the magenta pony, separated by a mint green pony that was to the right of both the yellow and violet pony in the last shot. When the spinning shot plays, pay attention to the left of the screen to see the wrong order of ponies.
Continuity mistake: During the "Stop the bats..." in the song, Rainbow is shown behind Flutter-shy, but when she walks in front in the same shot, the mane colours are swapped.
Continuity mistake: During the song, a bat spits out an apple that falls on its side. In the next shot, that same apple is upright.
The Return of Harmony, Part 2 - S2-E2
Continuity mistake: When the Mane 6 are running away from the changelings, before the fight scene, Applejack's hat disappears, reappears in the next shot, and then does the same again.
Continuity mistake: In Lesson Zero, when Twilight is going to collect the cupcakes, there are 12, then there are 10, and in the next shot the icing is all mismatched when it should be all pink.
A Canterlot Wedding - Part 2 - S2-E26
Continuity mistake: In the shot just before it goes back to Twilight and Cadence when they are about to escape, it shows Lyra Heartstrings in the crowd. When the shot does go back to Twilight and Cadence, it shows Lyra as a bridesmaid. Likewise, in part 1, Lyra is still a bridesmaid.
Continuity mistake: In the song, 'In Our Town', an earth pony spontaneously gets wings.
Answer: The smoke floats a few feet away from Twilight and close to the camera so you might think that the smoke is right in her face.
Lily Harrison