I thought of another one today. Sometimes fics with changing POVs or non-linear timelines can be confusing (even on paper). I was listening to a podfic today whose story has a lot of flash backs and I could never really tell when something was happening, there wasn't really any indication. With fic, some authors will italicize flashbacks or will use a divider to show a change, which can be missing in the audio version.

I've definitely seen podficcers handle this kind of thing well but it takes extra thought so I could see it turning some podficcers off of doing those kinds of stories.