In my latest book, "Manetho Demystified", I offer the theory that Hatshepsut started out her reign with a fictional Year 7 [to find out why this was a contrived number, you'll have to read the book]. I also made note of the fact that the combined regnal years of "Amessis" [the female pharaoh]. "Mephres" and "Misphramuthosis" add up to about 54 years [the total reign of Thutmose III from a primary source]. This is particularly true in an unccorrupted fragment  of Theophilius' copy of Manetho's 18th Dynasty, where he assigns "Misphrammuthosis" only 20 years and 10 months instead of the 25 years and 10 months given by Josephus.
Regardless it would seem that Manetho, the Egyptian historian of the Hellenistic Era, truly did believe that a queen, obviously Hatshepsut, reigned before Thutmose III. He has her ruling for 21 years and 9 months because he knew that the 9th month of the Civil Calendar [called "Pakhons" in the time of Manetho] was the month in which Menkheperre came to the throne. But he has the next king, "Mephres", ending his reign in the 9th month, as well. It seems quite probable that "Mephres" [elsewhere called "Misaphris"] and "Misphramuthosis" both represent Thutmose III but, because the latter had more than one prenomen at various times, perhaps Manetho did not realize they were one and the same. He may have even intended that "Amessis" and "Mephres" were co-regents, who ended their joint reign in the very same month of the year. In this, the Egyptian would not have been entirely wrong, of course. It just occurred to me that the difference between the 21 years of "Amessis" and the 12 of "Mephres" is 9 years. That could mean that the royal duo were co-regents beginning with Year 9 in the estimation of Manetho [but not mine]. My guess is this comes from Hatshepsut's mortuary temple at Deir el Bahari where Thutmose III is depicted as the junior partner of the woman-king at the time of her Punt expedition in her Year 9. Actually, the young man was shown many times in the temple, but perhaps the date "Year 9" was seen as the year of his advent as co-ruler. Thutmose III appears in the Punt expedition reliefs only once but they were surely deemed as interesting to people in the era of the Ptolemies as they are today. From such records men like Manetho attempted to reconstruct the history of their land. They did not dig into the ground for their information but worked with what was visible.
But it was doubtless confusing. Here was a pharaoh, famous from the monuments of his triumphant sole reign, not to mention a legend of folklore--at one time teamed with another. Not comprehending that the king had an independent reign prior to the usurpation of Hatshepsut, Manetho seemingly concluded that, in the 9th month following the demise of the female-pharaoh, he assumed his full birthright. Yet he erroneously [but understandably] considered nearly 13 years of "Mephres" accounted for within the years of "Amessis" and failed to give "Misphramuthosis" a long enough period of sole rule after the woman-king had vacated the throne. I cannot say, at this moment, how likely Manetho would have been able to connect the name of Maatkare to the female pharaoh, even if he toured the Deir el Bahari complex or could find an intact cartouche. Perhaps someone else has an opinion regarding this. At any rate, he didn't know the names of Hatshepsut. His "Amessis", more probably "Amensis" or Hmt nsw, must have come from some tale. Champollion expressed his own bewilderment at the temple:
If I felt somewhat surprised at seeing here, as elsewhere throughout the temple, the renowned Moeris [Thutmose III], adorned with all the insignia of royalty, giving place to this Amenenthe [Hatshepsut], for whose name we may search the royal lists in vain, still more astonished was I to find upon reading the inscriptions that wherever they referred to this bearded king in the usual dress of the Pharaohs, nouns and verbs were in the feminine, as though a queen were in question. I found the same peculiarity everywhere...