This question actually refers to Chapter 7 of To Kill a Mockingbird. Jem has discovered the ugly truth about why Mr. Radley cemented the knothole, eliminating the children's direct way of communicating with Boo. When Jem asked Mr. Radley about it, he was told that the tree was dying.
"You plug 'em with cement when they're sick. You ought to know that, Jem."
But later, when he asked Atticus about the tree, his father told him
"Look at the leaves. They're all green and full, no brown patches anywhere--"
Jem knew Atticus would not lie to him, but he realized that Mr. Radley had. Radley had cemented the knothole dliberately to prevent Boo from making any more contact with the kids. When Jem returned inside the house, Scout tells us that
... I saw he had been crying; his face was dirty in all the right places, but I thought it odd that I had not heard him.