The employer of your referee is irrelevant, so don't worry. A much more common mistake I see are referees being given that have very little or no bearing on the application. Sometimes a referee is included because the applicant feels it will reflect positively to have someone from their target industry listed.
What information in your application is the referee confirming? Academic, work or personal? If you assess a referee's suitability based on this criteria you have little to worry about as to your referee's employer.
