Goalkeeper Joe Murphy played despite clearly carrying an injury, thanks to the Football League's insistence on each sides involved in the competition naming six of the 11 players who have featured most this season.
The Irishman was replaced by Josh Lillis 12 minutes into the clash, and any aggravation of his problem lies firmly on the head of the suits at the League who are desperate to appease the latest sponsors of the most pointless competition in the English game.
"It's appalling that we are being told who we play when it should be our decision as long as we go out there and try to win the game," insisted Iron manager Brian Laws, whose side in the first round win at Valley Parade was actually more experienced than the Bantams outfit.
"We will appeal against (the fine) because on league appearances we had a far stronger side than they did."
Andy Keogh and Billy Sharp were both rested for the match, with Steve Torpey partnering Daniel McBreen up front.
The match itself was a dull affair, with Lee Ridley going closest for the home side with a stunning volley that was turned over by Joe Anyon.
And Lillis pulled off a close-range block from Michael Husbands. Jim Goodwin saw a second-half effort go wide of the post, but the tie was decided on penalties after a goalless 90 minutes.
And during the shootout the only player to miss was Iron defender Cliff Byrne, sealing a 5-3 win for the Valiants.
There were some familiar faces in the visiting ranks for the home fans - with former Scunthorpe players Michael Walsh and Paul Harsley playing the full game for the Valiants.
And former Iron loanee came off the bench for the away side.