When Jem goes back to the Radley place to get his pants, Scout decides she does not understand him as well anymore.
Jem loses his pants at the Radley house, and tells a lie to the adults because the kids are not supposed to be going there. That night, he decides to go back and get them. Scout desperately does not want him to go, because she thinks that Nathan Radley is going to shoot him. She does not want Jem to risk his life to avoid getting into trouble.
It was then, I suppose, that Jem and I first began to part company. Sometimes I did not understand him, but my periods of bewilderment were short-lived. This was beyond me. (ch 6)
Jem does not want Atticus to know about the pants because he thinks Atticus will be disappointed in him. Atticus has never whipped him, he says, and he wants to keep it that way.
Scout is too young to really understand what Jem is trying to tell her. This is why they are parting company. Jem is old enough to look at the world from an adult perspective. Scout is not quite there yet. She is beginning to realize that Jem is getting older, and they will not always understand each other any more.