The 19-year-old has not yet played a competitive match for the Gunners this season and underwent ankle surgery on Tuesday, which is expected to rule him out of contention until late February at the earliest.
Wenger, however, rejected suggestions this setback was the direct result of any one factor.
"You can blame yourself if you think people warned you be careful because he has a problem, but he had no problem," he said. "If you say to a player who is 18, who has no problem 'you don't play', he doesn't understand.
"It is difficult, especially at the end of the season we couldn't rest him at all because [Cesc] Fabregas was always injured and therefore it was more difficult to rest Jack.
"Maybe we played him too much, I don't know. His injury isn't necessarily linked with that."
Wilshere became the centre of a club-versus-country row over his intended participation in the European Under-21 Championships over the summer at the end of last season.
Wenger added: "I would like to show you the adversity we faced when we said he should not play in the Under-21s - most of the people wanted him to play in that, you should read the statements from people when we said he needs a rest."
Wilshere first felt the injury during the England international against Switzerland at Wembley on June 4. Wenger, though, insists all appeared well as Arsenal prepared for the new campaign with a pre-season tour of Asia.
He said: "We made a scan before we left and it was alright. This crack in the bone became worse and worse. People say to me it didn't heal because there is no blood supply, so it doesn't glue together any more.
"When you see the scan it looks like a little hole in the bone. We needed to screw that together because it would not heal.
"When he was in the boot it did not get better, it can be even worse. What they found was a very clean ankle and they came out very positive.
"Sometimes you are scared the player goes in and they say 'look, it was worse than what we expected', or they say 'it was better'. They said it was better than what they expected it to be."
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.
"We paid a heavy price in the Premier League for the quality of our performances in the Champions League. We had the bad luck to play twice away after the Champions League, and it's difficult for everybody," said Wenger.
Gervinho is suffering with a mild muscular problem and Koscielny has damaged his ankle, while Walcott limped off during Saturday's victory over Bolton with what was later described as a minor knee injury.
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