Most didn't make it to their seats until five minutes into the second half after a late rush for tickets sparked panic at the gates.
The attendance of 29,211 was bigger than Manchester City's for their UEFA Cup clash with Lokeren and was way above other Carling Cup crowds at Bolton, Everton, Middlesbrough and Coventry.
United chairman John McKenzie, in the Yorkshire Evening Post, said: "The fans of this club sometimes amaze me. For so many to turn out for what might be considered a low-profile fixture says much about their commitment.
"The trouble was that up to 3,500 people turned up after 6.30 seeking tickets, many of them wanting to pay at the gate. The last time we took cash in this way was in 1997.
"I am truly sorry that a small percentage of people were caught up in the snarl and they have my unreserved apology.
"But there are lessons to be learned, and the way to ensure full entertainment is to pre-book tickets and turn up in good time.
"I was staggered by the attendance and would like to thank people for supporting us at this difficult period in our history."