The main character Changez is referring to Erica's eyes in this quote. She starts to confide in him about having written a short story that she is going to submit to an agent for publication, but then he notices her eyes and feels like she's a bit "broken." To understand more deeply what he means by this quote, reading the next lines help as he explains it.
"...like a tiny crack in a diamond that becomes visible only when viewed through a magnifying lens; normally it is hidden by the brilliance of the stone" (52).
In this analogy, Changez examines Erica by comparing her to a diamond with a secret crack in it. Erica is the diamond and whatever her pain is represents the crack. He is interested in knowing how she became broken, or how she obtained the flaw or crack, but he is courteous enough not to bluntly come out and ask her what her issues are.