I think this PR will fix your issue – I had the same problem with shortcodes for the feed:
https://github.com/TheCraigHewitt/Seriously-Simple-Podcasting/pull/465
Problem is that when you get the content and the content has a shortcode that has a post ID – the global post id seems to be reset. Hoping to come up with a PR to fix this issue somehow.
Looking into the code a bit it looks like the plugin is just using the_title_rss() so it’s hard to believe the bug exists within the plugin, but can anyone else verify? If you embed a shortcode that points directly to an id, does the title of the episode within the feed change to the id that the shortcode is pointing to?