Server Version#: newest release
Player Version#: newest release
I have downloaded an Series with only one season but over 100 Episodes but I just noticed that Plex only shows 99 episodes and the 100th episode is shows as episode 0 and the 101st episode is shows as alternative version of episode 1.
Please answer the other questions first, before I can give a definitive answer.
By default, Plex expects all filenames of a tv show to include a season+episode code: s01e04.
If you have a season with more than 99 episodes, this will then have to be extended to s01e004.
But only for seasons with more than 99 episodes.
Different rules apply when using custom scanners/agents.