So this is a really strange issue I am facing, I think I tried everything. I recently loaded 21 seasons of Pokémon, as ordered per to the TVDB DVD order. However, for instance when I check any season like Season 15, I see all these missing episodes that I can only attribute to the episodes that would be missing if the show was ordered as per the Aired order on TVDB (since the missing episodes are ep.50-58).
I noticed that sometimes Emby will have merged S15E11 with like S15E30. Another minor issue I noticed is that many of the episodes may have the correct Title, and description, but the wrong TVDB episode ID.
I have TVDB as the highest priority metadata fetcher for the TV library, and do have the show selected as DVD order. My files are named as per the Emby standards.