The Arsenal boss also insists he has the squad to cope without the England midfielder for up to five months
The 19-year-old has not played a competitive match for the Gunners this season and yesterday underwent ankle surgery, which is expected to rule him out of contention until late February.
It is a much more serious prognosis than originally suggested when Wilshere - who played well over half-a-century of matches for club and country last term - suffered the problem in a pre-season friendly against the New York Red Bulls at the Emirates Stadium.
Arsenal will be without half-a-dozen first-team regulars for tomorrow night's Group F clash, including England forward Theo Walcott, Ivory Coast striker Gervinho and centre-back Laurent Koscielny who have all picked up minor niggles after Saturday's 3-0 Barclays Premier League win over Bolton.
Wenger, though, maintained there was no underlying problem in a packed Gunners treatment room.
The Arsenal manager told a news conference: "I don't think that the medical staff made any mistake on this case.
"It is unfortunate, we are all very sad at the club that it has happened to such a young boy.
"We were even more worried, but it was a big relief yesterday for everybody at the club that the operation went well."
Wenger continued: "The fracture he had didn't heal, what I have been told is that we had to go in quite quickly to repair it and that's why we decided to do it so quickly.
"He had an earlier fracture at the age of 16 that healed and around that he created another opening.
"Is it down to a kick, is it down to playing too much? I don't know, I am not a specialist, but that is unfortunately what happened. He told me he felt it the first time [when playing for England] against Switzerland."
Despite the loss of Wilshere, Wenger believes other youngsters such as Emmanuel Frimpong, can now step up to the challenge.
"It makes us a bit shorter in midfield and it puts a bit more pressure on our midfielders to perform game-in, game-out, because we will have less rotation possibilities, but every club can be tested on that front so it shouldn't impact our end result of the season and shouldn't be any excuse at all," he said.
"If [Abou] Diaby comes back well and quickly we should, number wise, quality wise, be all right.
"That depends as well on the injuries we have in the next two or three months.
"Touch wood we can absorb the number of games we face well and we have some younger players pushing like [Francis] Coquelin like Frimpong, who are playing very well, so hopefully we can cope with it."
Arsenal eased the pressure with their Premier League victory over 10-man Bolton on Saturday after what has been one of the most testing spells of Wenger's 15-year tenure.
In Europe, though, the Gunners have produced the goods, securing a place in the group stages with an impressive two-legged win over Serie A pacesetters Udinese and then coming away from Dortmund with a 1-1 draw after a late goal salvaged a share of the spoils for the hosts.
Wenger, however, is not expecting any easy ride against the Greeks, where he will serve the final match of his touchline ban.
"We are a train that started a bit late in the station, so we cannot afford to drop our consistency," he said.
"You never win easy in the Champions League - when you give absolutely everything, you have a chance to win.
"If you do not prepare properly, then you have no chance.
"After 14 consecutive years in the Champions League, if we have not learned that, then we are really stupid."
For Arsenal midfielder Mikel Arteta, this season is a first taste of top-flight European action following his deadline-day switch from Everton.
The Spanish midfielder, 29, is relishing the challenge.
He said: "It is hard to explain what it is about the Champions League, the atmosphere is different you are playing against the best teams in Europe every time.
"You are expected to win here, which is a really good thing.
"We need to be prepared for that and have to take things game-by-game. We all know we have the ability to do it."