Amy Pond had freckles, (TV: The Eleventh Hour) as did Compassion. (PROSE: The Book of the War, Warring States)
Lucy Sobel also had freckles, on her cheeks and nose, (PROSE: Slow Decay) and Robert De'Ath, on his forehead. (PROSE: Another Life)
The Ninth Doctor suggested to Blon Fel-Fotch Passameer-Day Slitheen that she would spare a victim because they had freckles. (TV: Boom Town)
Owen Harper suggested "freckles" as a nickname for Gwen Cooper. (TV: Day One)