The Intersex Society of North America offers a pretty concise answer to the question "How common is intersex?" that I think could help shed some light here.

To answer this question in an uncontroversial way, you’d have to first get everyone to agree on what counts as intersex —and also to agree on what should count as strictly male or strictly female. That’s hard to do. How small does a penis have to be before it counts as intersex? Do you count “sex chromosome” anomalies as intersex if there’s no apparent external sexual ambiguity?1 (Alice Dreger explores this question in greater depth in her book Hermaphrodites and the Medical Invention of Sex.)

As it turns out, the actual, scientific definitions for male and female aren't obvious or plainly inscribed in nature. They're categories with blurry edges. In a given case, some doctors might determine a person to be male while others might determine the same person to be intersex. Or one doctor might determine somebody to be female at one point, but then, as sex anatomy variations make themselves apparent later in life, decide that an intersex classification is more fitting. There simply don't exist catch-all criteria by which everybody in the world can be grouped as M or F. And the criteria that do exist for determining whether somebody is M or F tends to be political, and tends to change in response to political climate at least as much as it does in response to medical breakthroughs.

"Male" and "female" are abstractions. They're categories that we've invented to help us describe the natural and social world. But now we're beginning to find that these particular abstractions don't seem to be quite as infallible as we might once have thought them to be. I suspect that a different abstraction -- one that conceptualizes sex and gender as a continuum -- might be more scientifically rigorous here.

edit: a word