This seems to be a traditional feature of European werewolf lore.
The inability of evil shapechangers (such as werewolves or sometimes witches) to match all features of the creatures they shifted to resemble is pretty common in folklore. For example, in some Swedish stories, diabolical shapechangers could not grow a tail, even when they assumed animal shape; and therefore, they would sometimes run with one of their rear legs dragging on the ground, so it would look like a tail. The folklore about shapechangeres lacking of a tail makes a certain amount of sense, because humans have no external tails, but there are many similar stories about other body parts.
The eyes, in particular, were another natural choice for a body part that might not completely transform—and so could give away the shapechanger as a fake. One reason is that human eyes are, while not all that distinctive anatomically, associated very strongly with human nature. Our brains are extremely good at picking up on subtle cues coming from other humans—especially from other humans' faces. The eyes play a key role in this nonverbal communication, because they form part of the face, but also because (unlike the rest of the upper face) their movement can be controlled without moving any other body part. We can roll our eyes or wink without moving a muscle anywhere else, which gives our eyes unique capacities.
(Science fiction and fantasy actors wearing costumes that include thick masks or facial makeup often take advantage of the eyes' independent expressiveness to communicate with their audience. Ron Perlman here was known for doing that quite well in his Beast getup.)
Both the eyeballs' importance in human communication and their ability to move separately from the rest of the body (a sort of partial independence from the rest of the body) provide thematic reasons why they might not transform, even when the rest of the body does. Moreover, the eyes are also a well-known weak point (in humans and other animals) that a foe might want to attack. Many werewolf and other shapeshifter stories emphasized that the shapechanged creatures had substantial but specific weaknesses—and often those weaknesses were carried over from one form to the other. (Injuries sustained by werewolves in animal form could often be used to identify them even after they reverted to human shape.) The eyes being an important weak point again suggests that they might remain a vulnerability even after a villain has transformed into a beast or monster.
All the preceding points are just reasons why unchanged (or incompletely changed) eyes might be a features of a maleficent shapechanger. However, there are instances of werewolves being described with prominent eyes going back several hundred years. Trials for witchcraft (and available legal records of such trials) increase in prevalence in the historical record in early modern times (peaking in sixteenth and seventeen century). Werewolfism (and shapechanging) were common charges leveled against defendants in such proceedings. One of the most famous werewolf trials was that of Peter Stubbe, the supposed "Werewolf of Bedburg," in 1589. An pamphlet account of his trial was published, first in German, which was then translated into the English version that survives.
Under torture, Stubbe admitted to having been able to turn into a deadly wolf, thanks to the power of a belt he had received from the devil. His form was
... the likeness of a greedy, devouring wolf, strong and mighty, with eyes great and large, which in the night sparkled like fire, a mouth great and wide, with most sharp and cruel teeth, a huge body, and mighty paws....
While these eyes did not end up betraying Stubbe as a shapechanger, they are described in somewhat greater detail than the rest of his form. More importantly, there are described in a way that implicitly indicates that they were rather un-wolflike. In western Europe, wolves were often described as having small eyes. This is probably related to the fact that it was well know that wolves hunted primarily by smell, not by sight. Pigs, which also find food mostly with their noses, are also traditionally described as having small or dull eyes. Look at this 1811 illustration of one of Aesop's fables; note how much smaller the eyes are on the canids than on the other animals.
So "eyes great and large, which in the night sparkled like fire" suggests an unnatural pair of orbs, signifying the werewolf's evilly magical nature.