David Beeby, United's general manager, said the amount of tickets sold were around 5,600, including 2,080 Grimsby supporters.
He told the Scunthorpe Telegraph: "We knew we wouldn't have as many as for the first game, with it being on a Tuesday night and it is difficult for families with young children to be out at that time.
"There were some problems at the first game and people are a little bit wary of that.
"We are obviously trying to alleviate as many of those things as possible in terms of crowd trouble after the first game and make sure it doesn't happen again.
"There is still time for people to come and buy their tickets and we hope more people do and we get a good turnout."
Supporters have until 4pm tomorrow to secure a ticket for the game.