Mrs Baylock: Have no fear, little one... I am here to protect thee.
Damien: Please, Daddy! No, Daddy, no.
Father Brennan: He must DIE, Mr. Thorn.
Father Brennan: When the Jews return to Zion / And a comet rips the sky / And the Holy Roman Empire rises, / Then You and I must die. / From the eternal sea he rises, / Creating armies on either shore, / Turning man against his brother / 'Til man exists no more.
Answer: It's possible that the mark didn't appear until Mrs Baylock showed up and began teaching him about his heritage. The mark of the devil is said to appear only when Satan accepts a follower, and up until Mrs Baylock appears, Damien is a normal boy. Yes, he's the devil's son, but he knows nothing of his evil nature until she starts teaching him. In fact, at one point, Robert mentions that he knew every inch of Damien's body since he raised him and never saw anything, so more than likely the mark didn't appear until Damien had areas on his body where it could be hidden more easily.
dewinela
But it's a birthmark. He had it when he was born.