I wouldn't necessarily call it a bad episode, but one of the reasons the network stopped showing Invader Zim was the episode "Dark Harvest". It aired on April 20th, 2001 and was written by Eric Trueheart and Rob Hummel. The episode is about Zim stealing organs from the other children. That is probably why the network didn't like it. It was on a kids show, and let's face it, people back then (cause 2001 was so long ago) were more sensitive to letting their kids watch stuff like that. I don't know, I really like the episode.
https://www.youtube.com/watch?v=VnOBIwi9gLM