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.
Accidental Innuendo: Penny's father declares that he has "altered" Bolt. To "alter" an animal can also be a euphemism for neutering it.
All Animation Is Disney: Inverted, as many people mistake this for a Pixar film. In this case partly because after Sanders left the project, Disney brought in Pixar director John Lasseter, who influenced the film heavily in his own style.
Ugly Cute: Mittens, to a certain degree. She's a skinny cat humans would look on as a stray, after all. Surprisingly, it is also deconstructed: Since she's not cute in a conventional way, because she's half-starved from being declawed and unable to hunt, humans just tend to scare her away instead of giving her some food, and she's aware that the possibilities of being adopted after falling into a pound are extremely limited for her.
The Woobie: Both Bolt and Mittens can count as this.