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.
Crowning Music of Awesome: A 10-member live orchestra performs each episode, sometimes including other instrumentalists skilled in music from the region to which the pets are traveling during the episode. The show won an Emmy in 2008 for Outstanding Achievement in Music Direction and Composition.
Ear Worm: Good luck getting the theme song out of your head.
Family-Unfriendly Aesop - "Don't try to do anything on your own because you're doomed to fail." (In fact, this is illustrated in at least two episodes where someone tries to do a job solo and not only end up in a predicament of their own and are chided by the Wonder Pets who have to rescue them. In one episode, it's Ming-Ming who needs saving and states after that "I should have known better" than to try on her own.) Though likely unintentional, this is a constant message taught in every episode.
As if designed specifically to counter this, there is an story of the show called "KalamaZoo!," in which Ming-Ming travels to Kalamazoo to visit her aunt and is asked to look after her cousin Marvin. She thinks she needs the Wonder Pets' help, but is told that there sometimes are things you have to do on your own. This story is available on Nick Jr. on Demand and on DVD.
Fridge Logic: Ducklings don't stay yellow and fuzzy very long. Linny appears to be a mature guinea pig, and Tuck as a turtle can probably live for decades, so how many "Ming-Mings" have there been on the team?
Played with in "Happy Mother's Day!" - the Wonder Pets sing a song about Moms and that they have one thing in common, which Ming-Ming rhymes "They're all good at mommin'." Linny winces, but Ming-Ming insists that it's a good rhyme.
Viewer Gender Confusion - Apparently, Linny the guinea pig is a girl, but you wouldn't know it from the baseball cap and overalls, or the fact that she wears a blue cape, a color traditionally associated with boys. It doesn't help the other Wonder Pets seem to pronounce her name as "Lenny", when it's "Linny."