Louie's English Journal

In chapter 6 the relation between Scout and Jem has deteriorated very clearly since Jem prefers to play with Dill rather than her. “You’re gettin’ more like girl every day!.” In this chapter Jem goes into the Radley lot with Scout and Dill, though he is caught by a shadow, I assume is Boo, and they run away, there is a gunshot and Jem loses his pantaloons.  due to it being suspicious not to go toward the gathering crowd they join them, and Nathan Radley says he shot at a black person (phrased differently), but implies that he knows it was Jem. Jem sneaks back that night to get his trousers but is shaken up by something.i

I think that Jem was crying due to both, the inability to thank the person leaving these items, and that he realised it was Boo, and now he has lost the chance to communicate with him.