The forward scored both goals in a 2-0 victory, but the game was overshadowed by referee Roger East???s bizarre decision to send Brown off, even though team-mate John O???Shea had tripped Radamel Falcao.
In a statement released via the Professional Game Match Officials Limited (PGMOL), East insisted it was not a case of mistaken identity and he did in fact mean to send Brown off.
But Rooney, who played alongside both Brown and O???Shea for United, says the referee made a mistake.
???I don???t think it was Wes ??? it looked like Sheasy 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 played up front on Saturday afternoon and scored his first league goals of 2015 as United reclaimed third position in the Premier League.
And despite a run of games in midfield, the United skipper insisted he is happy to play anywhere for Louis van Gaal.
???I have done that throughout the years whether I???ve worn the armband or not. That???s something I have always done,??? he added.
???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.???
Asked whether the players??? understanding of Van Gaal???s philosophy was coming together, Rooney replied: ???Yes it does.
???We knew that obviously it would take time with a lot of changes and a different style of playing football. It???s probably taken a little longer than we would have liked.
???I think even last week we played well and didn???t deserve to lose the game but we???re getting there and if we can get into the top four this season we can really kick on from there.???