Hermione, believing that Harry had done something terrible, felt completely betrayed by him. Her anguish is further fueled by the fact that Harry refuses to answer Umbridge's questions, as he is protecting Sirius Black.
The scene where Hermione cries isn't a specific line of dialogue, but rather the combination of Harry's silence and the accusations against him, leaving Hermione feeling heartbroken and utterly distraught. This moment highlights the deep trust and love Hermione has for Harry, making her pain even more intense.