Rooney scored both goals as United defeated Gus Poyet's men 2-0 at Old Trafford, but the talking point after the game centred on referee Roger East's baffling decision to show Brown a red card.
United opened the scoring from the penalty spot when Radamel Falcao was brought to ground in the area after seemingly being tripped by Brown's team-mate John O'Shea.
However, East dismissed Brown and a statement from referees' governing body Professional Games Match Officials Limited later claimed that it was not a case of mistaken identity.
Rooney, who played with Brown and O'Shea at United, believes the official did make an error.
"I don't think it was Wes - it looked like Sheasy [O'Shea] so the referee has got it wrong and I'm sure they will look at that and rescind Wes' red card," he told Sky Sports.
Rooney's goals were the first he has scored in 2015, the captain starting in a more familiar striker role after a spell in midfield in recent matches.
Despite flourishing further forward, the England skipper insists he is happy to play anywhere for the team.
"I have done that throughout the years whether I've worn the armband or not. That's something I have always done," he said.
"I have played in midfield before I have played out wide before. At times you have to see what is best for the team.
"That is what the manager and I have felt and that's why I have been back in midfield. I love playing football and wherever the manager wants me to play I will play."
