All things aside—the story's a dud. A teenager born in Uganda to South Asian parents, who also lived in South Africa before moving to the United States as a child, checked the "African-American" and "Asian" boxes on a college application form that mirrors the United States's extremely specific and peculiar categories of identity. This is not newsworthy, regardless of the fact that it is, in fact, a true statement—as much as a person with multiple national and ethnic identities can accommodate a boilerplate college application.
Nothing here is untoward—unless one is operating under the strictures of a worldview that views both racial hierarchy and "college crimes" as issues befitting both breathless coverage and Deep Throat-level secrecy regarding sourcing.
That is, if you are the New York Times.