Applying to the wrong schools (OOS, too high, poor fit for school's mission).
Doing poorly in the interview including not speaking well, being rude to staff members, being weird.
Personality disorder (see "weird" above)
Applying very late.
Applying to too few schools.
Having poorly written application -- poor expression of ideas and/or poor grammar.
Lack of clinical experience.
Immaturity (you can be older and immature).
Unclear or poor idea of the purpose of a career in medicine.
Having only external motivation or wanting medicine for the wrong reasons (parents are requiring it, to make parents proud, job security with no passion for "the job")
Those are just some that come to mind.
Also, perhaps, an institutional action or criminal record that just can't be overlooked or out run.