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.
The scene where Joanna is stoned by the jealous women and her baby winds up being hurt by it.
The scene where the children win a Christmas tree, and Johnny helps them bring it up the stairs and leads the entire building in a round of "O Holy Night".
The moment where Francie realizes that Lee has been playing her.
The scene where Francie and her mother reconcile as her mother is giving birth, especially when Francie reads her mother an essay she wrote about Johnny after he died.
Francie's graduation, when she discovers flowers Johnny gave Sissy the money for before he died.
Unfortunate Implications: Several ethnicities/nationalities are casually stereotyped, but the Jews probably get it the worst of all. Sometimes it's Positive Discrimination, other times... not so much. Possibly from the filter of naive residents in an immigrant neighborhood that switched from being Irish and German in the story time to mostly Jewish when the story was written, so the writer would be unfriendly to them for 'taking the neighborhood'.
Plus Sissy scandalizes the family by having her tenth baby in a hospital with a Jewish doctor, citing her faith in Jews' higher intelligence and greater sympathy for women in childbirth. Confirming her belief, her baby is born seemingly dead, but Dr. Aaronstein revives it with oxygen. She even names the baby after him.