All passengers are required to have a chair for safety reasons. The chairs absorb a lot of impact in the case of a crash, and obviously they also have seatbelts which are important for safety.

I would rather sit in my seat with the belt buckled and not have another passenger bounce all over the cabin and hit me in case of turbulence. Not to mention capacity, balance and evacuation efficiency issues.

If the pilot doesn't know he has extra passengers, and those extra passengers add weight to the aircraft, and the aircraft is not fueled to handle the extra weight, that's a problem.