Of course it doesn’t.
Here are some points you need to know:
- The “Plex TV Series” agent is using the episode ordering from TheMovieDB.org by default ALF: Season 2 (1987) — The Movie Database (TMDB)
- You can switch to the default “aired” episode ordering of TheTVDB.com either globally for the whole library, or individually for each tv show.
- individually per show you can also switch to TheTVDB’s “Absolute” and “DVD” orderings
- if you change data on either TheTVDB or TheMovieDB, it will take usually 48 hours before the changes are available in Plex.
- Both websites have a policy which disallows to change the primary (“aired”) ordering to anything different than how the tv show was aired the first time. (Even if that was wrong, like it happened with “Firefly”.) If you change that, this will be reverted.
All you can do is to look up your show on both websites and pick one of the orderings which fit your files best. If you don’t find a “perfect” ordering, change the names of your episodes and re-sort them.