Pastis originally intended that Dickie the Cockroach would take the heads of people he didn't like, but editors felt this wouldn't go over well, particularly after journalist Daniel Pearl was beheaded by kidnappers in Afghanistan. Pastis changed the strips to have Dickie slapping duct tape on the mouths of people, instead. The original strips were included in later collections so that readers could judge for themselves.
Goat is a positive example, as early on the editors requested another character for the strip, and Pastis went through several animals before the Goat we know today was born.
Missing Episode: Many books feature comic strips that were never printed as they were deemed too offensive or simply not funny.
Old Shame: One book has several early strips that Pastis made when Pearls was still a webcomic. He derided most of them for being Out of Character.
There are also various strips that were Not Ready for Primetime and those Pastis thought were either too weird or just plain sucked, and ended up getting scrapped.
Recycled Script: Averted for the most part, but a pair of strips really stand out: September 29, 2011, a daily strip, was recycled less than a week later into October 02, 2011, a Sunday strip, with an extra punchline from Rat. This was pointed out in some of the latter strip's Gocomics comments.
Thesestrips as well, which ran about a month apart in 2008.
Shrug of God: Quite often, most notably with describing the crocs' dialect.
What Could Have Been: In the treasury book Pearls Freaks the #*%# Out, Pastis mentions at one point that he contemplated plans for a Pearls Before Swinemovie. It ended up not happening due to several Hollywood agents and executives not returning his calls.