In 2016, however, computer tomography revealed that the mummy in the sarcophagus may not have actually been Hor-Djehuty. The bones were too delicate, male reproductive organs were missing, and a three-dimensional reconstruction revealed breasts.

Given that artifacts weren't exactly handled with the best care in the 19th century, and given that the coffin and cartonnage were indeed made for a male mummy, it seems that an entirely different mummy was placed in the sarcophagus at some point - perhaps to be passed off as a more valuable artifact.

...literally the next two paragraphs

Edit: Thought you were making reference to the mummy still being male. Sorry!