Ghost podcasts appearing on smart playlist
I had been using the Podcast app, and then deleted it. I believe this left orphaned podcast episodes in the phone itself. I had to SSH into the phone and delete the orphaned files. I found this out when I switched to manually managing my music, and the "ghost" podcasts appeared on the phone (but not iTunes). 

I had earlier attempted re-downloading the Podcast app and re-downloading the "ghost" podcasts, but that didn't solve it.