Fast forward to DS9. In Apocalypse Rising, Sisko overhears a Klingon warrior who says he killed Sisko's friend from the Academy, a Benzite captain. Not possible if Mendon was the first Benzite in Starfleet, whoops.
Unless Sisko's friend was a Benzite Space Scuffling Force Commander who went to the Academy to get Starfleet credentials at an old age... Say, when Sisko was last at the Academy, doing his own command-qualifications course at the urging of Captain Leyton.
But yeah, that's an actual oversight, whereas "A Matter of Honor" is just an odd costuming choice. A bit like giving Captain Christopher or Khan Noonian Singh a Starfleet uniform, but not giving Miranda Jones or Samuel Clemens one.