Accidental Innuendo: There's one scene early in the play where Fabrizio looks down aghast at himself, motioning towards his legs. He's actually referring to his clothes, but the innuendo becomes even greater when one factors in the relevant line in Italian, where he says "She can't love a little boy!"
Alternate Character Interpretation: Margaret's failing marriage with her husband is often played differently. Some play it as their love burning out and becoming distant, others imply her husband is abusive and the distance is to keep herself safe.
Margaret's reprise of "The Beauty Is," and her enormous guilt for turning away to answer the phone when the pony kicked Clara, leading to her daughter being brain damaged.
Clara's realization that something is "terribly wrong" with her.
"No one with a dream should come to Italy."
Franca's response to Clara throwing a glass of wine at her during the Octet, after Franca kisses Fabrizio to make her husband jealous. The implication of course is that she isn't sure if Giuseppe would actually fight for her.
FRANCA: No, she is right. Right to fight for him. Please, everyone. Giuseppe and I are so happy for you both—Clara, Fabrizio. We should all fight for our love. I should —I would fight for Giuseppe.