Malaysia's Josiah Ng won the keirin gold after his team-mate Azizulhasni Awang, who crossed the line first, was controversially disqualified.
England's David Daniell was promoted to silver after Awang was thrown out for nudging Simon van Velthooven in a race that is traditionally full of bumps.
But all the controversy came in the keirin where Awang pulled his traditional wheelie in celebration as he crossed the line first.
However, judges ruled that he had impeded New Zealand's Van Velthooven in the final sprint and disqualified him.
BBC commentator Hugh Porter thought the decision was wrong.
"The rules are spoiling the keirin," he said. "The nature of the beast is six men fighting and bumping on the track.
"The best man won, but now he's not going to get his gold medal and that is a travesty."
Chris Boardman, a BBC Sport pundit and former Olympic cycling champion, added: "This is a beautiful event over-sanitised as far as I am concerned. I thought it was a great piece of craftmanship."