Gender, gender what is gender?

This article (and several similar articles in other journals) talk of the murder of a "transgender youth" who was a female (actually, the youth was living as a female) but had the genitals of a male.

What?

I will concede that sexual proclivities are not as easy to categorize as gender. And I will concede that genitalia aren't always consistent with one's sex (though the instances of this are very rare or they are very fake). But how can these journalists write such nonsensical sentences? A person is either a male or a female. Is EVERYthing relative or subjective to these idiots?