This is not unusual. It was mentioned above how insurance companies enter into contracts with pharmacies.

Another reason is that some pharmacies will prescribe enough medication to last for longer periods of time. For example I was stuck using a pharmacy I hated because they filled prescriptions for 90days at a time instead of refilling it 3 times at 30 day increments. By doing it this way the insurance company is paying for only one filling fee instead of three.