As a few of you have already pointed out, it looks like Sleepless in Ponyville on iTunes is pretty broken in the audio syncing department. Dialogue comes out noticeably earlier than the actual characters speak it (though some points seem alright). So far I have only tested the 720p verson to confirm it, but others have noted that different quality downloads are also suffering from the same issue.
Your best bet here would be to use the customer support feature within iTunes to report it! Hopefully we can get a clean upload soon. As much as the program loves to explode for me on Windows, their customer service is top notch.
Thanks to "A fan of the show" for originally pointing it out!