Continuity mistake: The Phantom and Diana take an airplane to escape the boat. Drax's henchmen shoot at it, touch the gas tank and gas starts flowing from it. You can only see gas two times, during close shots.
Continuity mistake: At the end when Billy Zane takes off his mask, the black makeup around his eyes "magically" disappears, even before the eyepatch section gets pulled from his face.
Continuity mistake: The bullet holes on the hydroplane disappear in the wide shots.
Continuity mistake: When the young boy crawls on the sea shore after being attacked by pirates, his hairstyle changes between shots.
Answer: She was preoccupied trying to escape from the bad guys and annoyed that a guy in a purple suit, was trying to save her, when she said, "I can do it myself." It was most likely later, in New York, when the met face to face. Kit and Diana, when she put two and two together. Again was too preoccupied trying to save the world to pause and confront him.