Scunthorpe closed the system down on Wednesday afternoon after "a number" of Leeds United fans tried to purchase tickets for home ends of Glanford Park.
A club statement read: "All orders will now be checked manually and any supporters who are not on our ticketing database (i.e. who have not purchased tickets for an SUFC game before) will be contacted.
"Those suspected of being visiting supporters will be given refunds in accordance with the terms specified on the ticketing website."
Checks will also be undertaken at the Glanford Park ticket office. Tickets go on general sale on Thursday from 9am, and are expected to sell quickly.
United have 700 seating tickets, and plenty of room in the Doncaster Road End left for the fixture that kicks off at 12noon on August 9.