You say a single scale? What substrate are you using? It is a possibility that it is a small bit of substrate under a scale too. It sounds more likely if it is a single scale than rot which is usually a lot of scales.

Scale rot is also often caused by injury or filth buildup in the enclosure, it is similar to trench foot in humans (sort of) it does not just happen it points to poor husbandry much of the time.