While you’re waiting for the cavalry, I’m curious if any of these episodes are being matched as duplicates of other, existing episodes. You can check in the Library view of your TV library by selecting “Episodes” from the view selection and then “Duplicates” for the filter:
You can then “Get Info” on a duplicate to see if it references the files you expect (or don’t):
If things don’t look correct there, you can try the Plex Dance on the offending episodes to see if that helps. After clearing caches as @JuiceWSA suggested, of course.
And at some point, logs (with debug enabled and verbose disabled) will likely be necessary.
