Wenger's men were already assured of qualification for the knock-out rounds alongside Borussia Dortmund ahead of Tuesday's 4-1 thrashing of Galatasaray in their final Group D game.
The result helped Arsenal bounce back from last Saturday's 3-2 Premier League defeat to Stoke City, but it was immaterial as they finished second in their European mini-league for the fourth time in five seasons.
Those struggles in the first phase have not helped Arsenal's cause as they have slumped to elimination in the round of 16 in each of the past four seasons.
And, while Wenger was pleased with Arsenal's response to the Stoke loss, he was left to rue their 3-3 home draw against Anderlecht - a game in which they led 3-0 - that has now proved costly.
"We came out strong and that's what I wanted from these players," Wenger told Sky Sports.
"There's a little bit of frustration that we have finished runners-up, but we knew at half-time we needed to score six goals without conceding.
"We won four games, lost one and had one draw. Looking back, we can maybe regret that point at home to Anderlecht.
"There's some great teams in the draw for the last 16 and we need to wait and see who we get."
Lukas Podolski and Aaron Ramsey each scored twice in Istanbul, the Welshman's second a stunning half-volley from 30 yards.
On Ramsey's wondrous effort, Wenger added: "When he took the shot I thought that was maybe not the best idea, but the way he took it, it flew in.
"The goals he is scoring is linked to his performances at the moment and that certainly helps his confidence to score goals like that."
