Fern has Asperger's Syndrome
For starters, she's an introvert, who at the beginning of the story has no child friends except her brother and prefers the company of animals to humans. A passion for animals is also a common trait among girls and women on the autism spectrum, as are intensely fixed interests in general. She daydreams in class, her uncle calls her a "queer child," and her mother worries about her solitude and animal obsession to the point that she consults a doctor about her. She also displays intense empathy and emotional sensitivity, which contrary to stereotype can be stronger
in people on the autism spectrum, especially girls. We see this when she saves the newborn Wilbur's life, seeing no difference in value between a piglet's life and a human baby's, and in how easily she cries throughout the story. The strange fact that she cries when Avery breaks the smelly rotten goose egg implies hyper-sensitivity to physical stimuli like strong smells too. She also seems highly intelligent, with an unusually sophisticated vocabulary for her age, and has at least one unique mental ability namely the ability to understand the animals' language, which none of the other humans share. Her eventual bonding with Henry Fussy and drifting apart from her animal friends toward a more "normal" social life might reflect the fact that for many children, Asperger's symptoms decrease or at least are more easily masked as they mature.
Jeffrey dies while they are at the fair
It explains why he is never seen again.
- A deleted scene shows him going to join his mother and siblings at the pond after the humans take Wilbur away. Hopefully he just realized he prefers living like a goose to living like a pig, and is just with his siblings offscreen in the end.
Charlotte didn't actually die until after Wilbur left the fair
This version differs from the book and the live action version in which the death of Charlotte appears to happen while Wilbur is still at the fair. I think she just moved off the screen to make Wilbur think she was dead so he wouldn't try to stay with her.
Henry fussy went to live with his grandfather because it was thought his mother abused him
At the end of the film Henry Fussy explains his disappearance by going to see his grandfather. His grandfather is shown to actually treat him in an age appropriate manner. Maybe it wasn't his choice. People may have started to talk when they saw how Mrs. Fussy treats her son. I think it is likely the state found out and began to investigate Mrs. Fussy for child abuse.