So I just started using Plex recently and I have found that any series that has 100 or more episodes only shows 99 and it will change what should of been episode 100 to now be episode 0 episode 101 will be episode 1 ect
Instead of having every episode in one folder just create a folder for each season and you won’t have any issues.
Season 1
Season 2
That’s how I have every TV series without any issues.
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name the way the guide says and it will see more than 100 episodes fine
S01E143