The irony of the femme fatale
The femme fatale is everything a man would want most. She's beautiful and alluring and powerful—but there's just one twist. She might be evil. By including a confusing, complex character like the Marquesa to be the murderess, the novel points to the confusing nature of gender roles and of romance.
The irony of plausible deniability
One would think that someone would need to be innocent to be innocent, but the rule of plausible deniability is that as long as you can preserve the illusion of innocence—even if it's a thin veil (literally)—that's enough to get away with whatever it is you're guilty of. That's certainly the case for the murderess, assuming the Marquesa is who killed the painter, because although every sign points to her, the men agree to let her keep her honor.
The irony of the blemish on the painting
The novel begins with a doctor assisting a patient in removing a blemish—one that he is actually fond of. When that blemish appears on a faceless painting of a woman with the artist dead in front of the canvas, it's ironic, because it seems that the blemish has become an even more powerful symbol than it would have been originally.
The ironic power of secrecy
By agreeing to be perfectly confidential, the Doctor quickly gains a new insight into the situation because he knows more than he's letting on. The irony of keeping a secret is that knowing something no one else does makes one want to brag because they'll feel powerful, but that small power is nothing compared to Dr. Malsufrido's power for knowing something no one else does. His secret helps him to navigate a murderer without endangering himself.
The irony of gender roles
The woman in the novel manipulates people into certain views of her that preserve their desire to help her, so by her seductive ability, she becomes powerful. The question raised is one of ethical implication—is it wrong for a woman to use her natural cunning to help herself? The murder notwithstanding, there is an interesting feminist issue about the lengths women have to go to in order to meet societies difficult requirements. The blemish removal scene might be likened to the practice of abortion—which would certainly have earned Dr. Malsufrido his reputation, by the way.