When Nicholas leaves Madeline's apartment for the first time, it appears to be in the basement. When he rushes to save her from marrying Mulberry Hawk, he runs up many flights of steps to get to the apartment.
As Nicholas and Madeline kiss for the first time, the angle of his head in relation to hers changes instantly across several cuts.
Just before Vincent Crummles announces that they're losing money with the current play, Mr. Folair can be seen grabbing the fire prop twice in two different shots.
The movie is set in the early-to-mid-1800s, but characters sing the hymn "God is working His purpose out" which was written in 1894, 24 years after the death of Charles Dickens.
Madeline Bray can be seen clearly with pierced earring holes. Pierced ears were not of regular use until more than a decade later. At the time, only rich women pierced their ears.
Nicholas's letter from Dotheboys to Ralph Nickleby carries a postage stamp. These did not exist in the 1830s.