The table seen at the very end of the film that the skull sits on is different from the table it is on through the rest of the movie. The table seen in the ending has no pattern, just horizontal wood grains. The table seen earlier has a pattern of hexagons.
When Dr. Christopher Maitland goes to murder his wife, the table in his study is shown again, but the book and statue are missing, showing only the skull of the Marquis De Sade.
In the first minute, the gate to the graveyard is swinging wildly, but the trees and bushes all around are still. (One random twig is plying about...) The phrenologist shuts the gate firmly. In the next shot, the gate is still and ajar, but the trees and bushes are moving about as if 'blown'.
When Maitland is holding the knife above his wife's head, you can see a clear cut between two shots, and Peter Cushing's character shifts from his original position.
The human jaw bone is not attached to the skull as they show this skull to be.
During the scene when the Skull floats to attack Peter Cushing's character, you can see the steel wires holding up the skull, in an "X" formation.
The girlfriend of the phrenologist is seen munching modern marshmallows in bed in the year 1814; although the ancient Egyptians invented the original recipe, marshmallows (in their present form) were not invented until 1850.