The rules page has 2 options that can affect how your check-ins function. The first, is "Duplicate Check Ins." If this is set to "Yes" duplicate check-ins are allowed. This is rarely used, but allows event organizers to track when an attendee enters a session and when they potentially leave if an additional checkin is recorded. This can be done by the user scanning the same checkin QR code on their way out or by the admin creating a second record for the user in the admin portal.
The other more useful option on this page is "Check In Session Time." This allows one to restrict check-ins to only be allowed within 15 minutes of the start/end time of a given session, or allow check-ins at any time. This can be activated to prevent fraud in situations where you want to be extra careful that your records show exactly who attended a particular session.