Brown was heavily featured in the Battle of Bramall Lane, a game where several Sheffield United players were sent off. He then left the field, apparently injured, in a move that raised suspicions of a deliberate attempt to get the match abandoned. This duly occurred when a second Sheffield United player left the pitch injured.

Brown was sent off after a two-footed challenge on Portsmouth midfielder,and former team mate, Sean Davis during a match between Fulham and Pompey on April 1, 2006. It was later revealed by Portsmouth boss Harry Redknapp that the two players did not see "eye-to-eye" together from their time at White Hart Lane.

Manchester United fans were incensed, after an intentional two-footed foul on Ryan Giggs in their 5-1 victory over Fulham on August 20, 2006. Brown received a yellow card for this. The normally unflappable Giggs then sought retribution, bundling Brown over from behind and getting himself booked, but drawing huge applause from the crowd.

Brown was once again in controversy after he stamped on Chelsea player Ashley Cole on September 23, 2006 during Fulham's match against them. This time, however, the tackle went unpunished by the referee.

In the penultimate game of the season against Liverpool on May 5, 2007, he head-butted Xabi Alonso. The referee did not see the incident and took no action. At a Disciplinary Commission hearing on May 10, 2007, Brown received a 3 match ban relating to this incident. He denied violent conduct but the Commission found the charge to be proved.