Correct. They are intersex. They are the exception that proves the rule.
“Proves” in that saying means “tests”, not “establishes the validity of”.
The legal maxim only makes sense in its domain because it rests on the idea that law is written by people, and that calling out a specific case for one treatment reveals a pre-existing understanding that outside of that case, that treatment would not apply.
Let's say you have concrete definitions of man and woman (and as many additional categories as you please). You see a person and believe they fall into one category. As it turns out, you are wrong, and they are actually in another category.
That you miscategorized someone has no bearing on the validity (or lack thereof) of your definitions.