This occurs because when Mrs. Bigio brings in the hot chocolate to the class, she deliberately walks past Mai Thi and does not let her take any, like the rest of the class. Mai Thi herself doesn't even reach to take any either. If you remember, Mrs. Bigio's husband was killed in the Vietnam war prior to this, and since this event, Mrs. Bigio has taken out her anger and grief on Mai Thi, who is a Vietnamese orphan who has been brought to the United States.
Seeing this, and understanding Mrs. Bigio's grief and sadness, but also thinking that Mai Thi is just as isolated and in pain, Mrs. Baker therefore secretly places her hot chocolate on to Mai Thi's desk so that she can have some and not feel left out. Mrs. Baker recognises the emotions of both Mrs. Bigio and Mai Thi and acts accordingly, giving her hot chocolate so that Mai Thi can share in the same pleasures as the rest of the class.