Here, I store my notepad files of each episode of My Little Pony: Friendship is Magic's animation mistakes. Keep in mind that the time stamps are based on my own videos, and therefore may not reflect accurately on your own. Follow an episode's link to its current mistake list.
The process I use to find these mistakes is simple: I open the episode with Quicktime and simply view it frame-by-frame. Every mistake I find gets a time stamp, followed by a description of the mistake. Moreover, you may notice some notes with stars (*) next to them. This is not a mistake but simply a note I made. These are more common this time around, since it allows me to keep track of more things during the episodes.
I occasionally upload a My Little Bloopers video on my youtube account to point out the major mistakes. The smaller and more common ones are left here.
That being said, I'm not perfect: if you know of any Season 3 mistakes I might have missed, then comment on it here!
Episode 1 & 2 - The Crystal Empire
Episode 3 - Too Many Pinkie Pies
Episode 4 - One Bad Apple
Episode 5 - Magic Duel
Episode 6 - Sleepless In Ponyville
Episode 7 - Wonderbolt Academy
Episode 8 - Apple Family Reunion
Episode 9 - Spike At Your Service
Episode 10 - Keep Calm and Flutter On
Episode 11 - Just For Sidekicks
Episode 12 - Games Ponies Play
Episode 13 - Magical Mystery Cure
Episode 3 - Too Many Pinkie Pies
Episode 4 - One Bad Apple
Episode 5 - Magic Duel
Episode 6 - Sleepless In Ponyville
Episode 7 - Wonderbolt Academy
Episode 8 - Apple Family Reunion
Episode 9 - Spike At Your Service
Episode 10 - Keep Calm and Flutter On
Episode 11 - Just For Sidekicks
Episode 12 - Games Ponies Play
Episode 13 - Magical Mystery Cure