Accidentally Correct Writing: Stephen Pastis drew Guard Duck ordering "Chateaubriand, cooked medium well, and a glass of your finest Pinot Noir". Pastis didn't know what Chateaubriand was, but assumed it was a food and felt it sounded fancy. Chateaubriand is a steak (more specifically, a thick slice of beef tenderloin in special sauce) and a good pinot noir isn't a bad wine pairing either.
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.
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 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.
Shrug of God: Quite often, most notably with describing the crocs' dialect.
Sleeper Hit: According to Pastis in an interview, this was the case for Pearls. The sales staff at United Features Syndicate didn't think the strip was going to sell, so it was placed online-only on the syndicate's website for about a year. What got it launched in newspapers was that Scott Adams, of Dilbert, was a fan of the strip and endorsed it on his newsletter. The readership increased as a result, and with Adams' support, the sales staff now had enough clout to get it sold to newspapers. It's now appearing in over 750 newspapers, has over a dozen book collections, and was even turned into an animated web series.