AMCAS makes the decision based on their guidelines. You can contest their decision if you want by sending them the course outline etc...
yes to what positron 511 said.
Basically you designate a category for your transcript class when you file AMCAS. When AMCAS review and process your application, they will check your classes, including the grades and class designation. They may change a class from BCPM to other. To contest the change, do what positron said.
Those are for borderline classes like psych. Med school pre-req and science department classes will have no problem being categorized as BCPM. "tough" as in tough luck if AMCAS doesn't accept the class as BCPM, but usually not tough for the classes I just mentioned.
Med schools would accept AMCAS designation of classes and BCPM and other class GPA calculations. Med schools would not re categorize and recalculate your GPA (no time and resource for med school to do that for thousands of app).