The worst incidents took place outside the ground following the match, but there was also an incident in the Don Cass Community Terrace following Lincoln's goal - it is believed that Lincoln supporters had gained tickets for the home end, they were removed and taken over to the Lincoln stand.
Bricks were thrown at police on Doncaster Road and Hilton Avenue, as officers had to wear protective shields, helmets and vests.
A Humberside police spokeswoman said: "The behaviour of a small minority of supporters - from both Scunthorpe and Lincoln - was disgraceful and did mar the occasion."