This is due to the way Mass Effect 3 imports faces. When Mass Effect 2 imports Mass Effect 1 Shepards, it takes the raw data to transfer the character’s face. Mass Effect 3 uses face codes generated by Mass Effect 2. However, Mass Effect 2 will not generate an accurate code when it imports a Mass Effect 1 face, therefore, when Mass Effect 3 tries to read the Mass Effect 2 save file, no face code exists.
According to BioWare community manager Chris Priestly, ”We are aware that some players are having issues importing the faces of characters from Mass Effect 1 or Mass Effect 2 into Mass Effect 3. The issue is likely in how faces were detected when imported from Mass Effect 1 into Mass Effect 2, and we’re working on the best way to correct it for affected players.”
As a semi-bypass, Priestly is suggesting to PC players a fan utility, Mass Effect Tools, which lets players compare the face to be used in Mass Effect 3 before they put it into the game.
Other fans have found that some of the import data was either wrong or missing. Hopefully, a future update will fix that issue, too.