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.
Awesome Music: The "Welcome Song" ("Gather 'round and sit right down, doesn't matter who you're next to...) and the class concert performance.
Toy Ship: Timothy x Yoko and Charles x Lily are practically canon. Claude x Grace could also be seen as this.
Viewer Species Confusion: Fritz. Is he a skunk? A badger? Nobody seems to be sure. Even looking at official reviews for the original Rosemary Wells book that he appears in, Fritz and the Mess Fairy doesn't shed any light on the subject. Publisher's Weekly calls him a "skunk," Kirkus Reviews describes him as a "badger." Presumably, this applies to Miss Appleberry (the occasionally-seen student teacher) by extension, as she appears to be the exact same species as Fritz.
The Woobie: The show loves doing this to Yoko. She has been teased about what she brings for lunch in "Yoko", had the Franks break her taketomobo in "The Taketombo" (they later fix it), and for her Japanese family figures being stolen in "Lost and Found" (they're later returned, though it's not revealed who did it).