Angst Aversion: The sequels are hard reads, with the ever larger number of character deaths in each one. Chauntecleer kills himself at the end of the second book, the rewrite contains a subplot involving Coop members turning on each other, and the third book ends with Pertelote and the other animals dying, although the blow may be softened by their reunion in the afterlife.
Broken Base: The rewritten Book of Sorrows (renamed Lamentations), which has been criticized for altering the characters, timeline, and tone of the series to make them fit events in the third book, published much later than the previous two, and causing a Continuity Snarl in the process. On the one hand, some readers are glad to see a clear-cut conclusion to the series and the reunion of the animals in the afterlife, but others are annoyed by what they see as watering-down of the characters and changes to important plot points.
Esoteric Happy Ending: A similar case to The Last Battle - at the end of Peace At The Last, most of the named characters are dead, although they are reunited in the afterlife, along with characters who died in the previous books.
First Installment Wins: An interesting case. The first book, The Book of the Dun Cow, is the most well known book in the series, receiving widespread critical acclaim as well as an off-Broadway theater adaptation. While the second was also well-received critically, its Darker and Edgier tone (even compared to the already dark first book) made it a tough read for some fans of the original. Then the author rewrote and cut large parts of the second book to fit the third book, leading to criticism from fans of the first two books as they already stood and making the third book, Peace at the Last, the most divisive of the three. It was quietly published in 2013 with almost none of the first two's fanfare or acclaim.
Cockatrice crosses it as soon as he grows up by murdering Senex rather callously and shoving the body aside.
The wolves' killing of Sweet Baby Blue and Jasper's murder of Chalcedony in Lamentations, which causes the other animals to exile them. Selkirk sees his eating Ratatosk as this and leaves of his own will.
A basilisk gets into the Coop and kills the Wee Widow Mouse by hiding inside the body of a Wild Turkey it killed.
At one point one of the worms that live in his head crawls out of Chauntecleer's beak in the sequel.
Tear Jerker / Crowning Moment of Funny: The last scene of the book, where Chauntecleer and John Wesley Weasel argue about who's going to join Mundo Cani under the Earth in fighting Wyrm somehow manages to be both simultaneously.