Following Barcelona's 2-0 victory at Real Madrid, Jose Mourinho implied the Catalan giants receive favourable treatment from referees and claimed the club had yet to win a "clean" European title under Pep Guardiola.
Wenger, who was handed a one-match ban for hitting out at Swiss referee Massimo Busacca after striker Robin van Persie had been sent off in the Camp Nou earlier this season, feels the comments were ill-advised.
"It's difficult for me to comment on that because we were involved in a situation like that," he said. "I refuse to believe that because, the day I believe that, it is impossible to manage.
"This season, they certainly had some advantages [but] I feel that they were accidental."
He added: "When a manager comes out of a big game like that, and you have a disappointment, you have to accept that you can sometimes that you go a bit too far, but I refuse to believe that there is, let's say, a script behind the stage and that Barcelona is advantaged.
"I feel that they over-react, certainly, but they play certainly the best football at the moment in Europe and you have to give them credit for that."
Messi is a big part of the reason for that.
Wenger guided Arsenal to a 2-1 victory over Barcelona at Emirates Stadium on February 16, before eventually losing the last-16 tie at the Camp Nou where Messi was again inspirational.
The Gunners boss cannot help be impressed by the Argentina forward, who scored all four as Arsenal were thrashed in Spain in last season's quarter-finals.
"Messi has qualities that are mental: humility, desire to play, happiness to help the team, always desire, you never see any bad reaction despite all the kicks he gets," Wenger said. "When you look at the numbers, you have to kneel down and say they are fantastic.
"When a guy scores 52 goals in modern football and 25 assists, when you see how difficult it is to score a goal, you just have to say it is absolutely exceptional what this player is delivering."