Why is Jerry so troubled? In chapter 18 "The Chocolate War"
Jerry is troubled because he fears the consequences of his rebellion against Brother Leon; additionally, he is both tormented by the oppressive atmosphere of the school culture and by his inability to fight back effectively.
Sickened by Brother Leon's cruelty and the physical intimidation perpetrated on the students by the Vigils (an in-school secret fraternity), Jerry feels an instinctive urge to rebel. When Brother Leon demands every student sell fifty boxes of chocolates for the yearly fund-raiser, Jerry objects. He is supposedly under Vigil admonition to refuse for ten days before he submits to Brother Leon's orders.
Yet, after the ten days are up, and Brother Leon calls his name again, Jerry's answer is still a deliberate 'no.' Jerry himself is shocked by his own audacity; his anxiety is so palpable that he feels himself in a claustrophobic trance, buried alive under this oppressive culture of intimidation, terror, and self-hatred.
Like many of the boys, he despises the order of things at Trinity, but is helpless to effect necessary changes. His rebellion is a great cause of anxiety for him; he doesn't know whether he is doing the right thing by this lonely rebellion amid almost universal conformity among the boys. He doesn't know whether he can endure all the notoriety, disgrace, and almost certain suffering of being the one lonely rebel that will be held up as an example of insubordination. Worse of all, he doesn't even know whether his one stubborn 'no' would be an effective and worthwhile rebellion against Trinity's power structure. Jerry is in quite a tough spot.