The nameplate on Elizabeth Medina's tomb goes from looking almost brand new to worn and rusty and back in several different shots.
As the pendulum is being brought down, it eventually slices open the shirt. In one of the following overhead scenes, the shirt is no longer sliced open.
When Elizabeth Medina starts to open her coffin, her hand reaches out and grabs the side edge, but in the next shot, her hand is gone.
When Nicholas pretends to be dead, Elizabeth talks to him and moves his head towards her. In the next shot she moves his head again to same position.
When Elizabeth (Barbara Steele) follows Nicholas (Vincent Price) down to the dungeon, her lover Dr. Leon (Antony Carbone) comes in too. When she first gets to the top of the steps, her mouth is covered in lipstick. When she gets down the steps to her lover and they kiss, the lipstick is completely gone.
The musket which Nicholas has in the cupboard is pre-loaded. (He is about to use it until stopped.) The gunpowder in muskets moistened if left for any period of time (and therefore wouldn't fire anyway and so would have to be unloaded again before use) so were stored unloaded until needed.
The main character, Nicholas Medina, claims to be the son of an Inquisitor. The Spanish Inquisition was formed by Catholic clerics who were not allowed to have descendants. However, though Catholic clerics were not "allowed" to have children, there are many documented instances of priests, bishops, and even popes having sired children.
There is a discontinuity with the previous shot when Dr. Leon tells the sister how her mother was tortured.
When Nicholas screams "true" when finding out his wife was buried prematurely, the next shot is discontinuous from the previous; his facial expression is changed, especially the mouth.
At the beginning, when Francis pushes the door which the servant tries to close in front of him, a discontinuity is obvious.
When Nicholas is talking to Francis about Elizabeth in front of her portrait, there is a discontinuity from prior shots, when he starts talking about her singing.
None of the torture instruments that appear were used by the Inquisition, and many of them didn't exist during the time the story is set. One of the most clear examples is the iron maiden, which was invented during the 18th century.
The story takes place in 1545, as indicated by the date on Elizabeth's tomb; however, in the background in one scene, a grandfather, or longcase, clock can be seen. The longcase clock was not developed until 1670.
When Francis shows the others the trap door he discovered, a modern hinge can be seen, although somewhat covered by paint. This type of hinge wasn't available in the mid-1500s.
The portraits of Nicholas Medina's father and Elizabeth are both painted in a very expressionistic fashion using strong and sometimes heavy brushwork to achieve the desired appearance. European portraiture and any subject matter done in the 16th century was painted with translucent layers of pigment to create the desired effect. The style of painting of these portraits and the wall paintings of figures in the dungeon are styles developed centuries later than shown here.