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)
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.
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: 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.