The short answer is, MapRun simply punches controls that the runner approaches, without any extra logic considering what is the next control on the course. It also doesn't do a review of the punches and add extra punches. (MapRun Admins can edit results - but the system doesn't do that itself).
The definitive guide to punching is at:
http://maprun.250607.n8.nabble.com/Punching-Controls-What-are-the-Rules-tp201.htmlPeter