How do we know if it was an illegal stop?

My son was driving a car registered and licensed in my name. An officer ran the license plate, and pulled him over. When asked why he was pulled over, the officer responded with the: running of the plate and it shows his license is suspended. When I asked the officer what he was pulled over for, he told me the same thing. I asked, "If it’s my car and registered to me, how can it be that something pops up on my son?" The officer explained that he has been associated with the car in the past for a violation, and that $45 is owed on a reinstatement fee to Secretary of state, he's driving on a suspended license. I told him that's a mix up, every payment has been made but one was late. He was issued a ticket for driving on a suspended license.