Nothing official has been said yet as such, but speculation (and best guess) is that Imane Khelif has a disorder of sexual development such as 5α-reductase deficiency (5-ARD). This is a DSD that affects only males. It inhibits the differentiation of male genitalia during fetal development, possibly resulting in a boy having external female morphology, but male reproductive anatomy internally.
This is the same DSD that the Olympic runner Caster Semenya has. Semenya was required to take testosterone-suppressing medication to be eligible to compete.
So while there's no hard evidence at this time that Khelif has 5-ARD or any other DSD, the situation is a bit more complicated than, say, The Lia Thomas situation: a Transformer stealing awards from female athletes because he was a mediocre competitor in the male class. That said, a person with 5-ARD is by definition a male, and should be disqualified from competing in female categories.
If nothing else, this controversy is giving the Internet a crash course in intersex conditions, which may have the side benefit of debunking some of the trans fairy tales.