That isn't a Jellyfin thing, Plex has the same issue. And both Jellyfin and Plex give you mechanisms to resolve that issue (using the alternate episode ordering

That isn't a Jellyfin thing, Plex has the same issue. And both Jellyfin and Plex give you mechanisms to resolve that issue (using the alternate episode ordering that the metadata provider has, rather than the default one, or using another metadata provider if need be).