Racism and warfare
To Jones, there are essentially two wars: World War II, which is happening in Europe at this time, and the silent war of racism in America. He has nightmares about both of those, and they define his experience of injustice. He is sent to the war to avoid getting charges pressed for his gun possession, and since he views himself as the oppressed party in a combat, he was intending to kill white racists with that gun, so he himself has become violent. The moral of the story is that chronic mistreatment and constant injustice finally corrupted his character.
Sexual mistreatment
Madge wants to have sex with Jones throughout the novel, but Jones understands that she's clearly just using him to fulfill some sort of humiliation game. Since she is a bitter racist, having sex with a black guy represents her masochistic desire to be humiliated and degrade. When Jones turns down her insulting offer, she waits a day and then when they are alone, she screams that she's being raped. Jones runs away, knowing no one will trust him.
Then Alice herself mistreats him, too, by making him humiliate himself before the white racists before she will sleep with him. Jones is a real victim of sexual misbehavior, but it isn't the kind of abuse that can be demonstrated or proven easily, so it goes without ever being fixed.
Power and race
Jones is disturbed when he learns that one simple indiscretion (yelling at a subordinate employee) would mean the end of his role. He is demoted from his leadership role, even though he had reason to lose his temper; the woman was being racist and disrespectful, even using racial slurs to disrespect Jones. This shows that even though Jones was "in-charge," he was still subject to the powerlessness that racism imposed on him, because everyone still looks down on him and ignores his point of view.
