A win would have sent the north Londoners joint top of the Premier League with Manchester United and Manchester City going into the new year.
However, the point leaves the Gunners in third place in the table and Wenger bemoaned the fixture schedule which he felt helped their title rivals.
"We had a disadvantage that Manchester United has not got - Wigan played three days ago and we played 48 hours ago, a big game in the evening," Wenger added.
"It is a point and we will see at the end of the season how important it is - last night Manchester United played 1-1 at Birmingham and we played 2-2 today."
Wenger, whose side visit Birmingham on New Year's Day before taking on Manchester City at the Emirates on Wednesday, continued: "It was disappointing because we were 2-1 up, playing against 10 men and dropped two points.
"But overall it was a difficult game, very physical, with a high level of commitment from Wigan and they caught us a bit at the start.
"You always felt any mistake at the back and we could pay for it as long as we didn't score the third goal."
Martinez upbeat on season prospects
Wigan manager Roberto Martinez declared himself "extremely pleased" with the result but criticised N'Zogbia for his red card.
"There's no excuses - that's unacceptable, it's a bad reaction," Martinez stated.
"Charles started the game very well, he won a penalty, he gets kicked in every game and there's a lot of emotions but you cannot accept that sort of reaction.
"He let his team down - football is a team game and the reaction of the players got Charles out of jail in that respect. We'll deal with it internally but it's something I don't like.
"Sometimes in football you need to react in the right manner even if you are getting kicked all over the place.
"From the first minute Charles got a rough treatment and you want to protect the skilful players and that protection should come from other areas not from himself."
Meanwhile, Martinez insisted Wenger's decision to make so many changes had not aided Wigan.
"Not at all - looking at them they are all full internationals with really good experience," the Latics boss explained.
"I would have preferred to play against the team that played against Chelsea and it would have been practically impossible for them to have recovered."
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