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Season ticket holders, loyalty card and supporter club members were able to purchase tickets beforehand but were restricted in the amount they could buy.
But there have been claims made by fans - including on the Iron-Bru.net messageboard - that some of these supporters bought up more than their permitted amounts, meaning some fans were left ticketless.
Wharton has promised to look into the allegations, if anyone can provide evidence that the rules were not followed.
He said: "If the system was abused it will be investigated. I am confident that all season ticket holders and loyalty card members were properly catered for.
"I would like some positive evidence that anyone was able to purchase more than four tickets per person when the tickets went on general sale.
"In one or two cases, such as sponsors, they were allowed to purchase more than four tickets and in some cases one person may have queued on behalf of a number of season ticket holders and loyalty card holders so that their tickets would be together."
The current ticketing system was introduced after the FA Cup visit of then-Premiership Leeds United two years ago, when season ticket holders and loyalty card holders could buy as many tickets as they wanted.
Tickets were being sold on the black market in the town, a number of forgeries were made and fans were stood outside Glanford Park on the day of the game in a vain bid to get a ticket.