The Elements of Harmony (2) - S1-E2
Other mistake: At the end of the episode when Princess Celestia is talking to Twilight Sparkle you can see that Princess Celestia's tail is on top of her leg instead of in-between. It's covering her cutie mark.
Other mistake: During Pinkie Pie's 'Smile Song', there is a scene where Pinkie Pie is jumping on a skipping rope (jump rope). Initially, the rope is held by two other ponies. However, at one point, these ponies are no longer holding the rope and the rope is just floating there. It isn't held by unicorn magic otherwise there would be a glow that appears when a unicorn holds something with magic, neither is anyone's horn glowing.
Baby Cakes - S2-E13
Other mistake: During Pinkie's Piggy Dance, she pokes out between the two babies. The female baby shifts over, then a lump appears on her chest that should be her front right leg. However, the lack of a line makes it appear to be on her chest.
Other mistake: During the song, as the cardboard tree falls, Apple-Jack lifts her hoof in a way it couldn't possibly bend.
The Elements of Harmony (2) - S1-E2
Other mistake: When Celestia is standing over Luna, her cutie mark looks elongated.
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