score:8
For clarity, there isn't a "wrong number of people," there's a mismatch between the manifest (number of people that are supposed to be on the airplane) and number of bodies aboard.
It must be reconciled. How depends on company procedure and practicality. Some things I have seen:
I've seen it a couple of times where children boarded as lap children are seated on a less than full flight. I figure it's because they're counting empty seats to accommodate stand-bys, so they end up with a seat count mismatch.
The most important regulatory issue is the count matches in case recovery is required. It's important to know who is onboard but this is less of a "security" issue since presumably any person onboard was screened at the terminal entrance.