Diaby scored the winner for Les Blues in their opening qualifier in Finland last month in his return to the national side.
Wenger believes that Deschamps should have shown more patience with his player.
He said: "I said many times that if France wanted Diaby in Spain (for the World Cup qualifier on October 16) they should not take him for Finland and Belarus.
"They could have taken him but not played him because the guy has been out for a year, played four or five games.
"You have a breather, give him two weeks to recover completely. I think it was a mistake to play him with the French national team."
Diaby will be out for at least three weeks with the thigh problem, and begins his spell on the sidelines when Arsenal face Olympiakos in the Champions League on Wednesday.