Graham Alexander was furious at Ben Toner's decision to concede a goal for Crewe last weekend.
Benn was dragged down by home defender Mickey Demetriou in the build-up, leaving Omar Bogle free to score. However, no action was taken at that time.
The Bantams have sent footage of the incident to Professional Game Match Officials Limited (PGMOL) for their opinion on the incident.
Alexander went to see Toner after the match and asked for his opinion on what the City manager deemed a red card offence.
The club has already lodged a complaint with the refereeing body over impunity and mismanagement of strikers Andy Cook and Vadin Oliver this season.
The incident with Ben looks even more vivid.
“I spoke to (PGMOL national group director) Mike Jones a month and a half ago about some of the challenges that are occurring with our players, especially Andy Cooke and Vadin Oliver. It was ridiculous,” Alexander said.
“But the Jay Ben case was an act of violence to me. The players actually grabbed him by the scalp and dragged him to the floor, and the spot where they scored was the position Jay Ben was supposed to be defending.
“I know they can’t see everything but there are four referees and it’s a set piece so they’re all there so they only see one side.
“It was a failed challenge, it's not a good challenge and it shouldn't be on a football pitch.
“But at the moment it doesn’t look like that’s going to happen, so we’re going to have to roll with the punches.
“We overcame that with a fantastic win in Stockport, but we must continue to overcome all the other challenges in front of us.”
The absence of VAR outside the Premier League means off-the-ball events can be missed, but Alexander was surprised that no one from the refereeing team saw what was happening. That's what it means.
“It's in a box and we have four officers watching over it. We know how difficult it is because there's a lot of bodies in there.
“But the two players were pretty isolated at the back post and weren't in the group.
“I don't want anything to do with it. I then spoke politely to the referee and asked him to look at it and give me feedback.
“I didn't ask about his (Alex Pattison) red card or my yellow, I just wanted to highlight the issue.
“I also sent a video for clarification because that wasn’t correct, so I’ll wait for your feedback.”
City and Crewe are facing FA charges over a dispute between players over Pattison's sending off. You must send your reply by tomorrow.
Benn was given time off for the Virtu Trophy trip to Stockport, with Brad Halliday starting in his place in the right wing-back role. The Lincoln loanee is expected to return against Swindon.
Alexander added: “He uses his physical data to get a ton of results. His distance and strength are just incredible and he’s great every day in training and in games.
“We were going to leave him out completely, but we wanted to try Brad in his normal position.
“He has played as a right centre-half and left wing-back for us, but given his training methods and current situation, we would like him to compete with Jay Benn for that position. .
“It was a good opportunity to give him a chance to feel like he's a part of what we're trying to do here in his natural capacity.”
Halliday scored Stockport's second goal in City's 3-2 win when his header aimed at keeper Colin Doyle missed the target. But Alexander felt the club's Player of the Year bounced back well.
“He conceded the second goal but I thought he bounced back and his performance in the second half was first class.
“He's been in and out, so it was understandable that he was a little rusty at times. But he's a great player, a great professional, and we think very highly of him, so I I’m happy for him.”
