Some of the iTunes U and Podcast items I’ve previously deleted from my iTunes library were still appearing on my Apple TV 2. It turned out that the iTunes library (on my desktop) had not completely deleted it’s references to those items.
To cure the problem…
create a new iTunes Smart Playlist and set it to match on “mediakind is iTunes U” (substitute whichever media kind is given you phantom appearances after deletion).
If you find the offending item displayed in this smart playlist, you can confirm that it’s really gone from your hard disk with a right click & get info. An error would indicate that you’ve already deleted it from disk. After NO on iTunes offer to locate it for you, iTunes will then display the last information it had in the library database (which will include the last file path location).
Now that you’re sure you’ve found the phantom entry, you can permanently remove it by selecting the entry in the Smart Playlist and using OPTION + DELETE.
The item should now be gone from the display lists on your Apple TV 2.