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Jamie Mackie’s dramatic injury-time winner earned the U’s a vital 1-0 win over their fellow strugglers, lifting the side out of the Sky Bet League One relegation zone.
But the goal was overshadowed by confusing scenes when the officials appeared to overrule the strike and take play back for a goalkick at the other end.
That came after Lewis O’Brien had gone close to putting Bradford ahead – and there were some suggestions that Davies had initially even awarded a penalty for a challenge in the United area.
The protests from both sides lasted around four minutes before the referee went with his original call.
Bowyer said: “It was absolute carnage.
“Their centre half wipes out (Eoin) Doyle, which is a booking. The ref allows play on, which is fair enough.
“The ball goes across and O’Brien goes to tap it in the net. According to Lewis, he doesn’t think he’s touched it, so it’s gone out for a corner.
“The ref should go back and book (Curtis) Nelson, which he doesn’t, but gives the goal kick.
“There are players in the penalty box, which you’re apparently not allowed to have, and it didn’t go out the penalty area.
“They then go down that flank and the linesman stands still level with the 18-yard box and he’s talking down the mic about not taking the goal-kick properly.
“They have a shot that ricochets off (Jerome) Sinclair’s back. Richard O’Donnell has got it covered and then Mackie volleys it in.
“Then all chaos commenced. Three quarters of their dug-out were all the way down by the corner flag and nothing happens about that.
“So, the referee in terms of the rules and regulations has completely lost it.”
To add to the confusion, Mackie, who had already been booked for dissent, thought he was going to be sent off after finding himself amongst the fans as United celebrated wildly.
He said: “I kind of got dragged into the crowd a little bit.
“It’s obviously an amazing feeling when you score the winner late on and the emotions were high.
“I thought ‘oh no, he might have interpreted that as over celebrating’ and he pulled me over and I thought ‘oh, second yellow, it is what it is’.
“And then when he said about disallowing the goal, I couldn’t believe it.
“I just said you need more time to call a goal off of this magnitude.
“You need to have a little bit more clarity than just speaking to one of your officials.
“Why don’t you take a little bit longer, which thankfully he did and he came to a conclusion and we’re just buzzing we’ve got the three points.”