These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Not to mention that his crusade got every animal from the woods homes destroyed.
Director Displacement: Despite being claimed as "A Wes Anderson Film", there were actually two directors. Anderson directed only the voices while animation director Mark Gustafson did all of the animation (and spent more time on set while Anderson would give directions through e-mail). The film's cinematographer even questioned Anderson's role on the project.
Foe Yay: Rat with Mrs. Fox. "Am I being flirted with by a psychotic rat?!"
Fridge Horror: Mr. Fox said that the tranquilizers were enough to sedate a gorilla. You're probably thinking, "But if it's that powerful, won't that KILL a beagle?" Well, considering that we don't see any of the beagles (except the rabid one) after that...
Ho Yay: With the Ambiguously Gay portrayal of Ash, his interactions with Kris can be read in rather interesting ways in the second half of the movie, especially when he forces Agnes to go away just to talk to Kris. What makes it even funnier is the fact that they are cousins...
Jerkass Woobie: Ash isn't a bad person at heart and obviously has a lot on his mind. On the other hand, he's shockingly cruel to Kristofferson, sinking so low as to crack jokes about his extremely ill father with him in the other room.
One-Scene Wonder: Owen Wilson's character of Coach Skip functions as this, appearing apparently only to explain (if at all) the rules of Whackbat.
Petey, whose only spoken scene is a song sung by his Ink-Suit Actor Jarvis Cocker. Especially funny for fans of Jarvis who might recognize the dancing.
They Changed It, Now It Sucks: Numerous British people complained about the film's "Americanization", as the humans are British and the animals were American, when everyone was British in the book. None of the Americans seemed to care.
Again, the use of American voices for the animals and British voices for the humans added contrast.
And even made fun of America, in a way, since the difference between the humans and animals is that the animals are "wild", the American accents belong to the "uncivilized" side.
Plus, only the farmers are portrayed as bad, there are other british human characters shown that are not evil, like the reporter and possibly Petey.
Squick: Taken Up to Eleven with details of how the farmers stink, don't take baths, have horrible-tasting disgusting food, etc.
Uncanny Valley: To some, the realistic fur and eyes on the puppets can be unsettling.
That and the fact that they might look just like the animated corpses of roadkill.
The humans... oh god, the humans...
The Woobie: Petey looks like he really needs a hug after Bean berates his song.