When Atticus questions Tom about his encounter with Mayella, Scout recognizes the difficulty of Tom's situation. When Mayella essentially tried to force Tom to kiss her, Tom didn't want to disengage himself too violently because he didn't want to hurt her. His only choice was to run, but that would, in the eyes of many of Maycomb's citizens, indicate a sign of guilt.
When Mr. Gilmer questions Tom, Scout also recognizes that Mr. Gilmer will use Tom's prior conviction of disorderly conduct against him.
As Mr. Gilmer continually tries to manipulate Tom with guiding questions, Dill gets sick and Scout takes him outside. Dill explained that he didn't like the way Mr. Gilmer was treating Tom:
“Well, Mr. Finch didn’t act that way to Mayella and old man Ewell when he cross-examined them. The way that man called him ‘boy’ all the time an‘ sneered at him, an’ looked around at the jury every time he answered—”
Despite Mr. Gilmer's manipulation's, Jem is quite confident that Atticus will win the trial. Having been so confident, Jem was extremely upset at the guilty verdict. Although each child discerned troubling things about the way Tom was being questioned and his predicament in general, Jem, being the oldest of the three children, seemed to understand the travesty of the situation more fully.