It took Sunny a long time to perceive the anomaly for several reasons. To begin with, it was so subtle that it was almost impossible to notice. His whole mind was concentrated on the thoughts of battle technique and styles, and still, he only saw it by accident.
The second reason had to do with his decision to face the Stone Saint without the augmentation of his Aspect Ability. Because of it, the shadow had nothing to do. It returned to acting as a proper shadow and obediently repeated his every movement while he fought.
The last reason was Effie — or, more specifically, the fact that she had brought a source of light into the hidden lair, making the shadow actually visible.
Because of this unlikely combination of events, Sunny was able to see it.