The Scope of the Xperiment
At the beginning of the story, the reader learns that the scientific experiment involving X costs billions of dollars, and the instruction manual assembled by the scientists is thousands of pages long. That all of this money and effort is put toward raising a gender-nonconforming child is ironic because it emphasizes the difficulty of putting into practice something that is quite simple in theory.
Mixed Up
At the end of the story, the psychiatrist determines that X is the least "mixed up" child he has ever encountered. This is the story's ultimate irony, as the parents of the Other Children have labeled X a disruptive and unstable influence at school. In reality, X's gender-nonconforming upbringing has allowed X to develop into a strong and capable child who is, according to the psychiatrist, more mentally and emotionally stable than their peers.