What situation do both Atticus and Scout recognize?

Atticus actually reveals several themes throughout the story.

The most obvious and important being prejudice.

This is shown many times. He shows how ms. dubose was not the grumpy old

crone they thought her to be, and rather a fighting drug addict who conquered her addiction. He helps Scout realize that Boo was just an agoraphobic neighbor who lived his life through the children. There are other examples too.

Basically, he reveals that people aren't who they seem to be.