I remember passages where she describes herself as abnormal, regarding her ladyparts. She may have a working female anatomy, but she alludes that she has more. She might have a penis, or part of one. It doesn't really say.
I don't remember any serious indication there was something abnormal about Elpaha's genitals in the book. I'll drop it, though, unless someone actually comes back with proof.
There is a moment when one of Elphaba's lovers remarks that he believe he sees something unsettling concealed by her pubic hair, and that Elphaba has taken great pains to conceal SOMETHING about herself.
A description of the character on wicked.wikia.com says:
"Five years later, she unexpectedly meets with Fiyero, and the two begin an illicit love affair, ultimately conceiving a child together, a boy named Liir, which is not reveled until Son of a Witch. During the affair, Elphaba refuses to allow Fiyero to see her naked. They only make love in the dark. Eventually, Fiyero does see her naked, and sees a scar between her hips. This is never explained, but several times in the novel, it's hinted that Elphaba was born with male parts. She was mistaken for a boy at birth, and in the introduction, her possible hermaphroditic body is gossiped about."
The passage about her groin is page 196, while she sleeps with Fieryo, the only lover she takes that is indicated in the book -
Her pubic hair grew, almost more purple than black, in small spangled curls, a different pattern than Sarima's. There was an odd shadow near the groin - for a sleepy moment he wondered if some of his blue diamond has, in the heat of sex, been steamed onto her own skin - or was it a scar? But she woke up just then, and the in moonlight covered herself with a blanket. She smiled at him drowsily and called him, "Yero, my hero," and that melted his heard.
When she's born (page 20), we read -
"Another willful boy," said the fishwife, sighing. "Shall we kill it?" "Don't be so nasty to it," said the crone, "it's a girl." "Hah," said the bleary-eyed maiden, "look again, there's the weather vane." For a minute they were in disagreement, even with the child naked before them. Only after a second and third rub was it clear that the child was indeed feminine. Perhaps in labor some bit of organic effluvia had become caught and quickly dried in the cloven place. One toweled, she was observed to be prettily formed, with a long elegant head, forearms nicely turned out, clever pinching little buttocks, cunning fingers with scratchy little nails.
No problem. I don't know if it's settled? I mean, to me it is, but I can't speak for anyone else.
Here are a few further thoughts - Since we're never given any indication that Wicked's narrator is unreliable, I think we have to take the birth scene as fact. Yes, the crones were confused because they thought they saw a penis, but they didn't. Let's not forget they were so mesmerized by the penis that wasn't really there that they didn't even notice at first that the child was green.
I think the repetitions that suggest any "confusion" about her gender/sex/reproductive organs, etc., are to speak to larger myth-making of the Wicked Witch that happens, showing the origin for some of even the most outlandish myths about Elphaba but I still remained unconvinced that they are nothing by myth.
I know people who were convinced that even Elpahba's death in the book is ambiguous (though the subsequent books easily lay that theory to rest) because of the final lines - "And there the wicked old Witch stayed for a good long time." "And did she ever return?" "Not yet."
Again, I think it's all about the way myths are created than it is about actual tangible evidence that she was a hermaphrodite or that she didn't actually die.