Duplicate seating can be quite common. It can be caused by two or more people being checked into the same seat at the exact same time, or if someone is already checked in and they are resseat-assigned into a seat that someone is already checked into.
It us not always picked up by the staff at the boarding gate as you are boarded by your sequence number. The sequence number is the order in which you have been checked into for your flight.
The paperwork/headcount will always match the number of pax onboard a flight.
Under normal operating circumstances - you cant check in too many pax for a flight - unless all pax were checked in and there was a cycle swap to a smaller size aircraft.
I hope this helps.