The acceptance of upper level courses to be used as fulfilling prereqs varies widely across both schools and conditions for course substitution
1) Most schools have stated policy that only the specified prerequisite courses can fulfill the requirement similar to below example
http://www.upstate.edu/com/admissions/faqs.php
Can other science courses like Organic Chemistry II or Microbiology be used to complete your prerequisites?
No. We will not accept any other science courses as substitutions for our required prerequisites.
2) Most conditions affecting this policy revolve around AP credits
-
Some schools will accept AP courses as fulfilling prereqs so long at the course/credit appears on your official college transcript with no additional work required, though it is often recommended
http://www.upstate.edu/com/admissions/faqs.php
Do you accept Advanced Placement credits?
Yes, as long as you were awarded college credit and the course(s) are listed on an official transcript from your primary undergraduate institution. The Admissions Committee recommends that you also complete advanced science coursework in order to be competitive for admission.
http://sls.downstate.edu/admissions/com/requirements.html
Do we accept AP credits for our prerequisites?
If your undergraduate college has awarded you AP credits and the credits are listed on your transcript, we will also accept your AP credits to fulfill our prerequisites if the course is listed by subject title on your final official college transcript. However, in order for the Admissions Committee to consider you to be competitive for admission, you should take advanced level science course work equivalent to the number of credit hours which have been accepted for AP prerequisites.
-Some schools will accept only certain AP courses (usually Bio and Physics) but not other courses
http://weill.cornell.edu/education/admissions/app_faq.html
Do you accept AP credits for prerequisites?
We accept AP credits for physics only. Requirements for other courses must be met by taking advanced science coursework.
https://www.urmc.rochester.edu/education/md/admissions/applying-to-rochester.cfm
Advanced placement courses may meet only one semester of the chemistry and/or one semester of the physics requirements. Advanced placement will not satisfy the biology or non-science requirements. Upper level courses may be taken to satisfy these requirements.
-Please note
-Substituting upper level courses without having meet a stated condition for doing so, may not accepted by a particular medical school
-Prerequisites are typically not checked for fulfillment until after you have taken an offer of acceptance during the pre-matriculation phase
-Most schools have dates by which a course must be completed in order to matriculate. This used to be just immediately prior to medical school orientation but with classes beginning earlier and earlier, this date is becoming sooner in the cycle such as June 1 or even Jan 1. This prevents acceptees from completing a missing prereq in the summer prior to medical school
-Schools vary widely in their waiving or appealing the requirement, some being extremely strict and other being very open to substitution.
-In sum, it is up to you to know the school's requirements/policy and have fulfilled them prior to required dates. Schools can place you on deferral and even withdraw an acceptance for failing to do so
