One reason why Stephen has trouble mortifying his senses is his soul. There seems to be something deep within Stephen that prohibits him from domesticating his desires and acting according to the religious precepts that have been presented to him. In chapter 3, Stephen prays and tries to shut out the memories of his sinful behavior and their concomitant senses. Unfortunately for Stephen, his soul will not cooperate. There's an intangible yet powerful part of him that refuses to let go of his sordid experiences. "The senses of his soul would not be bound," says the omniscient narrator. There are moments when Stephen feels he succeeded in closing the door on his senses. Moments later, his soul reopens and shows him all that he's done.
In chapter 4, Stephen continues to try to mortify his senses. He subjects each one to "rigorous discipline." As with the fitful prayer, this program fails to squash his "childish and unworthy imperfections." Soon, Stephen rejects Catholicism and the type of asceticism that it demands. As the narrator says, Stephen's "destiny was to be elusive of social or religious orders." Stephen's fate requires him to confront and learn from the assorted senses of the world, not to try and suppress or avoid them. Stephen isn't built to passively follow the wisdom of a priest. He has to amass his own knowledge and wisdom. To do this, he has to face "the snares of the world" and engage with the senses that it imprints upon him.