"É um menino."
Technically, "He is a boy" is a correct translation, but by excluding "ele" the phrase becomes contextual. "He" or "She" would have to be implied from previous sentences, but we know we are talking about "He" because of the word "menino" (you dont say "She is a boy").
I think it's a bit unfair to mark that question wrong..perhaps you can just note the distinction upon grading..
Technically you do not need "ele" to say "he is" since the verb conjugation itself already gives you the context (i.e. "sou menina": I am a girl. No need for the "eu"). A student would not imply that the question before was "what is it?" hahaha... Seems funny they haven't changed it. It is, however, comical to imagine someone looking at a child and saying "what is it?, such a strange looking thing!"