Neither skipper Cesc Fabregas nor fellow midfielder Samir Nasri were involved in the 0-0 draw at St James' Park during his debutant Gervinho was sent off for slapping Joey Barton as Barcelona and Manchester City continued their respective pursuits.
Wenger confirmed that both men remain Gunners players for now, but voiced his frustration at the prospect of losing them.
He said: "Yes, we are concerned by that because when you take players at 16, 17, 18 years old and you play them in the Premier League, you need to be brave.
"But you do it first of all because you think they deserve it, but secondly as well because you think the club will be rewarded when they are 23, 24 and are in a position to deliver.
"It is a concern, of course - but if the financial fair play comes in, I think we will be in a very strong position. But at the moment, it doesn't exist."
Of more immediate concern for Wenger is his side's failure to make the most of their dominance on Tyneside before late controversy changed the shape of the game.
The main talking point centred around one man who was courted avidly during the summer and another whose continued presence on Tyneside remains in some question.
Former Magpies target Gervinho's evening ended badly when he was sent off 14 minutes from time for aiming a blow at transfer-listed midfielder Barton.
The Newcastle man angrily confronted the Ivory Coast international after he had gone down under Cheick Tiote's challenge inside the box, intimating that he had dived.
In the resulting melee, the £10.5million striker lashed out and was dismissed by referee Peter Walton with Barton, who was also involved in the incident which saw Abou Diaby suffer a similar fate at St James' last season, receiving a yellow card for his role.
Asked for his view of the incident, Wenger said: "I think I saw more than the referee, and that is two yellow or two red, not one red and one yellow.
"There is a link between the two incidents - he [Barton] gets away with it. That's the link. Last year and this year, he gets a yellow card."
Barton ended up on the ground in the incident, and Wenger was less than impressed with the reaction of a player who also appeared to be stamped on by Alex Song in the first half.
The Frenchman said: "I wouldn't like to comment too much on that incident because I don't think it gives any credit to the Premier League.
"But you know as well as I do that he has not been hit hard enough to lie down for two minutes.
"But I cannot influence that and I am not really concerned by it."
Opposite number Alan Pardew, however, had a different opinion.
The Newcastle boss said: "Firstly, Gervinho dived, I don't think there's any doubt about that, and that gets the blood boiling in any footballer, let alone Joey Barton.
"Then of course it turned into a tussle, but Joey never raised his hands or anything and the guy slapped him around the head.
"You can't do that. You know on a Sunday morning, you can't do that, so you ain't going to get away with it here, so I thought the referee probably got it right."
The unsavoury incident marred a hard-fought encounter in which the visitors failed to make the most of their dominance with substitute Theo Walcott coming closest to finding a winner with a 64th-minute shot which was saved by goalkeeper Tim Krul.
Newcastle might have snatched victory at the end had Laurent Koscielny not managed to get ahead of Peter Lovenkrands in front of goal, but that would have been harsh on the Gunners.
Wenger said: "The regret is we missed something in the speed of our passing in the final third, but overall we had a very solid performance because I can't remember that we gave a goal chance away, and away from home, you have to give credit to our team for that."
Barton defended his actions in his clash with Gervinho.
"What do people want me to do, stand and trade blows with Gervinho. If u raise ur hands to players (sic) faces, u should be off. Ref got it right." he posted on Twitter after the game.
He added: "If i stayed up or went down its (sic) not relevant, raises his hands off. I was merely highlighting he struck me. Song stamped should of (sic) been seen."