We usually count our pax and check for any discrepancy on the PIL. It is very easy on Short and Medium Haul and in First because there is a limited number of pax. In bigger cabins we simply count the pax after T/O. After that you would immediately spot any ''new entry'', since you got to know the pax in your working zone.
It didn't happen to me often, usually on SH-MH, and every time politely informed the pax he made a mistake and asked to move back to the original seat.