Skin lesions have a wide variety of causes. The most common causes of skin lesions are injury, aging, infectious diseases, allergies, and small infections of the skin or hair follicles.Chronic diseases such as diabetes or autoimmune disorders can cause skin lesions.Skin cancer or precancerous changes also appear as skin lesions.ommon causes of skin lesions. Changes in the appearance of the skin can result from common conditions such as: 1  Acne. 2  Boils and carbuncles. 3  Folliculitis. 4  Freckles. 5  Nevi (moles) and other benign skin growths.