Rival fans were kept apart inside Sincil Bank but in the city centre traffic ground to a stand still as police kept rivals sets of fans apart.
Shortly afterwards there were sporadic outbreaks of violence as Lincoln and Scunthorpe fans came to blows.
Three fans were charged with public order offences after the match while the rest were released without charge.
A Lincolnshire Police spokeman said officers had maintained a strong presence both during and after the match.
He said: "This sort of behaviour is unacceptable. It spoils the spectacle for the genuine fans who go to enjoy the game."
Lincolnshire Police believe a small number of trouble makers may travel to Scunthorpe without tickets and have sent a strong warning telling them to stay away.