According to Dr. Thomas P. Connelly for The Huffington Post, there is a variety of reasons for people biting their cheeks, including physiological causes, pure accidents or a psychological basis. Cheek biting may pose an oral hygiene health risk due to causing painful mouth sores that could also become infected.
Dr. Connelly mentions that physiological causes can include misaligned teeth or temporomandibular joint disorder, also referred to as TMJ. These, as well as accidental bites during normal chewing, may produce skin lesions on the inside of the cheeks.
According to WebMD, such wounds are called stomatitis. They are painful and may affect a person's ability to eat, talk and sleep properly. Wikipedia includes psychological-based cheek biting under the blanket term "body-focused repetitive behavior," or BFRB. These are various physically harmful compulsive behaviors arising from a weak or faulty control of one's impulses.