In the scene where the Cantor prepares to whip the 13-year old Jakie, the boy has three buttons conspicuously pinned to his shirt for most of the take. However in the shot where the cantor shoves him towards the bedroom, there are only two buttons.
Before the dress rehearsal "Jakie" applies black face and he misses a portion on the upper right forehead. He dons the wig which covers the white spot. After he returns from the dress rehearsal and removes the wig, there is no white spot. It is covered with black face.
When Jack is writing the aforementioned August 7 letter to Mary following the Cantor Joseff Rosenblatt recital, immediately after he writes the words "nearly stopped," there is a splice in the film (but not the soundtrack) and the insert of the writing is repeated at an earlier point so that Jack writes the same sentence again. This may have been to allow for a reel/disc change, since there is a conspicuous pause of silence in the middle of the shot where the music cue ends and another begins.