Wenger's relationship with Gunners supporters reached an all-time low at the weekend when they railed against his substitution of Alex Oxlade-Chamberlain for Andrey Arshavin.
Captain van Persie also appeared to react to Wenger's decision with the word "no".
And the move backfired badly as Arshavin failed to prevent Antonio Valencia from setting up Danny Welbeck's winning goal in a 2-1 victory for Manchester United.
However, Holland striker van Persie has clarified the situation and also revealed the teenager had picked up a calf injury.
He told The Sun: "I was not having a go at the boss on Sunday - I was just sad to see Alex leave the pitch as he just gave the assist for our only goal.
"I was not questioning his judgement - I know it's not my place to challenge what Arsene Wenger does...
"Alex-Oxlade Chamberlain had a calf injury. We did not know that but the boss did and brought Andrey Arshavin on."
He added: "The manager and I are fine and my relationship with the club is good.
"There is no problem, there is no conflict and there is no controversy.
"The boss knows that, I know that and the players know that."
