The baptism scene and the death of the children
Instead of a traditional baptism, the children undergo a tragic, ironic baptism that ends with the end of the baby brother, and gives the baby sister polio which ultimately takes her life as well. So the baptism ends up being a kind of anti-baptism, leading to death instead of life.
The irony of incest
It's not a normal thing for a man to become sexually obsessed with his own daughter. In fact, it's so potent that the wife detects it within the first few years of their daughter's life. This irony is maybe less ironic in light of the age that Materia was when they were eloped.
The irony of attraction to young girls
Perversion is essentially ironic because it involves the unlikely, unexpected misfiring of regular things. Instead of having a healthy, confident sexuality, James's need for affection drives him to seek out the innocence he associates with young girls, and the youth is fascinating to him. Ironically, his valid, understandable need for approval and love morphs into an indefensible willingness to exploit innocence instead of actually meeting his needs.
Dramatic irony in Materia's suspicions
When Materia discovers that James might not be trustworthy around her daughter, it constitutes dramatic irony because the reader already understands Materia's predicament to be the result of the same problem in James's marriage to her. His sexual perversions are what got Materia in the marriage to begin with. Another ironic aspect of this is that James probably doesn't love his wife very much after all, since he still feels such need for another girl—a young girl no less.
The irony of having more children to dissuade pedophilia
Materia's strategy for keeping James distracted from his obsession of their daughter involves having three more girls. This may not seem very wise, but it does mean James will be alone with one girl less frequently, because more people will be around to witness something if it happens. Perhaps this is part of what drives him to enlist.
