Well, this is a common problem I heard from many iPhone users. Obviously, you cannot transfer some iPhone podcast files with iTunes due to the copyright issue or something like that. Therefore, you'd better use a third party tool to transfer podcast from iPhone to iTunes and here I recommend TunesGo.
TunesGo is a specialized tool being contributed to transferring podcast between iPhone and iTunes. As a constantly evolving software, it is compatible with almost the whole series of iPhone, including iPhone 6/6 Plus/5s/5c/5/4s, and certainly, it will be still leveled up to support the rapidly updated iOS devices.
Run TunesGo after setting it up on your computer. Plug your iPhone into the PC with USB cable and your devices will be detected by the program automatically so that you can read the files on your phone in details.
Step 2 Move iPhone podcast to iTunes
Click the "Podcast" button in the left panel to view all podcast files on your iPhone on the right side. After right-clicking the item(s) you want to sync, the transfer is done by selecting "Export to" > "Export to iTunes Library".
Using TunesGo, all podcast on your iPhone can be transferred to iTunes Library in incredible efficiency. Furthermore, it also works in transfer between iPhone to iTunes regarding music, movies, music videos and playlists.