My first guess would be infection. Ninja often move through dirty areas, and the bandages and wrappings may get torn. Its important to make sure the injured area remains clean and switch the bandages often.

Similarly, high amounts of activity can tear the stiches or rip the skin apart again. Its that kind of repeated damaging of the skin that causes the worst scaring.

Of course, some wounds will scar no matter what. Deep wounds, or those in places with little skin like the hands and feet, are more likely to cause scars.

There are instances when ones own personal chakra gets in the way of a wound healing correctly, or when enemy chakra can sap one's natural healing, but that is much rarer than simple rambunctious students getting into more trouble.