Will people please quote me on this for the next hundred times when this question comes up. Schools do not simply use a transcript to verify course requirements have been met and they do so after acceptance but prior to matriculation.
1) Schools only see the courses you enter on AMCAS when they are considering your application for admission. AMCAS does not verify online or do they do anything to check for prerequisites which is a school specific function.
2) Official transcripts are required be sent directly to the school when you are accepted but are not the only way that courses are checked during post-admission/pre-matriculation phase.
3) During a school's "due diligence" of an acceptee they will frequently use the National Student Clearing House (NSCH), which has agreement with AAMC/AMCAS a few years ago. This organization has the largest and most update database on official college course catalogs and other registration material now dating back about 25 years, a large fraction of which note course section number that may indicate if a class was online or not
4) Additionally, schools may contact UG registrar for it's pre-matriculants to check on courses including if any sections were online or not.
