I'm having this same problem. I use the iPad Remote app to select TV shows that are ripped and tagged in iTunes, and the wrong content plays when I select an episode. I discovered today that this is also a problem viewing iTunesU content. In the case of iTunesU, I assumed it was a sorting order issue in the app, but in the case of TV shows it is often the case that a completely different show than the one I selected -- one not in the list -- will start to play.
I am running the current version of both iOS for Apple TV 2 (v4.4), and Remote.app for iPad (v2.2).
I have discussed the cause and work around to this problem in the below post:
Simplest work around: copy the Episode Number into the Track Number, and Apple TV will play the correct episode. In short, Apple TV thinks TV shows are songs when controlled by the Remote App.