Make sure you are following the recommended naming conventions which can be found here:
TV Series: https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/
Movies: https://support.plex.tv/articles/naming-and-organizing-your-movie-media-files/ (just for good measure even though you didn’t mention movies).
I do not know how big of a deal would be, but one thing I see that you are doing incorrectly is using s##-e## instead of the recommended s##e##.
Without actually seeing examples of your directory structure it is hard to say if that might be your issue, but starting with the link above for TV series is a good place to start.
Depending on the issue, you might need to Plex Dance the files (either just the episodes, the whole season or the whole series, really depends on what is not showing).
I can tell you I have Supernatural and Star Trek: The Animated Series and they both are showing in my library properly.
-Shark2k
