Twilight and Flash Sentry share a few intimate moments (hugs, looks,)
The songs sung by the three villains "Battle of the Bands | Under Our Spell | Welcome to the Show" are pretty suggestive for a children's movie; among them are hips moving and dance numbers. In 'Battle of the Bands' the lead singer touches people's heads and cheeks throughout the song.
It could be unintentional, but at least one time each, Rainbow Dash's and Sunset Shimmer's breasts are momentarily larger than usual. It might happen to more of the characters, but I only noticed it with those two. They're quick and hardly noticeable scenes. If you aren't looking for it, you probably won't see it.