When I took my Kaplan course
they said the same thing. The USMLE scoring process is not transparent. They do admit to using experimental questions so there will invariably be some questions on your exam that dont count but you won't know which ones they are and its entirely possible that the USMLE also doesn't at the time your exam is generated, know which ones they are.
Since the process is not transparent the advice is to mark every question to the best of your abilities and after a few minutes if you have no idea whats going on - to quote Dr. Stephen Daugherty from Kaplan - "Mark your favourite letter and move on"