Futurama is a hot mess of a show because of how Fox butchered the original broadcast order.
This [latest] season has alternatively been titled the ninth season (production) and the twelfth season (broadcast). This list follows the previous season box sets, which feature the episodes in the original, intended production season order, ignoring the order of broadcast.
I would recommend picking a convention (production or broadcast) and sticking with it. It looks like tvdb prefers the former (hence only 9 seasons)
what agent and scanner are you using on your Plex TV library?
also make sure no other agents are overriding your chosen agent in the Agents section of the server settings. maybe local media assets are overriding it or something.