You have to add each subfolder separately. like image below
What happens is Plex expects the next folder after the one listed to be a show folder but instead it is seeing Tv 0-999 which it then thinks files inside are all the same show. Since it cn’t glean anyting from the folder name TV 0-999 it looks at the first file it sees ( one of the 12 monkeys) which it can glean info then it only starts looking at the episode numbers of everything else in tv 0-999 and merges them in to the same show.
