IPhone – Podcast ep on iphone 5s will not delete

The podcasts part of iTunes just manage those you have either subscribed to, or subscribed and unsubscribed but still have episodes. It looks like your issue is related to trying to manually manage these, which will let you add the files to your iPod, but iTunes really doesn't know about the structure behind them.

I would recommend having it manage them for you. In that case, you can also tell it to delete those (or keep those) you want after you listen.

For example, I have a couple of concerts from NPR on my iPod that I keep, but my other daily/weekly podcasts delete after they have been listened too.

I expect the reason you are seeing the difference between iTunes and the iPod is the way you are currently mixing the two methods.

You could create a smart playlist that excludes files that are already included in another playlist.

So, in your case if you generally sync a playlist called "At Work" whcih contains what you normally sync, but then also throw a few others into the sync too, you could create a smart playlist that looks for any ticked track that is not already in the "At Work" playlist. Call this "Adhoc" or something, and add this to your sync list, and you should have a new playlist that shows anything that wasn;t part of your original sync list.