The Premier League leaders were beaten 2-0 at Napoli on Wednesday which allowed Borussia Dortmund - who edged winless Marseille 2-1 - to seal top spot courtesy of a better head-to-head record after the trio all finished on 12 points.
That meant the German side will be seeded for next week's draw while runners-up Arsenal face the prospect of a last 16 clash against either Barcelona, Real Madrid, Atletico Madrid, Bayern Munich or big spending Paris St Germain.
"Of course to finish second makes the potential draw more difficult, in the last four or five years we have had very difficult draws, so maybe this time we will be more lucky," Wenger was quoted as saying by Arsenal.com.
"But if you look at the teams who are potentially there, at least we know we will have a difficult draw."
Arsenal were set for the point they needed in Naples to secure top spot before one time transfer target Gonzalo Higuain put the Italians ahead in the 73rd minute.
Arsenal captain Mikel Arteta was then sent off shortly after with Jose Callejon adding a second in stoppage time as Napoli fell one goal short of the required victory margin which would have sent them through at the expense of the Londoners.
Wenger's relief at advancing was tempered by the realisation that winning Group F would have meant Arsenal being drawn against one of Bayer Leverkusen, Galatasaray, Olympiacos Piraeus, Schalke 04, Zenit St Petersburg or AC Milan in the last 16.
"That is the frustration because you feel there was room to do better but it could have been worse as well tonight," Wenger said.
"We will see what comes out of the draw and will assess that in February (when the first legs of the last 16 matches are played) because a lot can change on both sides, on us and the team we play against," he said.
"So we need to put that to the back of our minds now and focus on the Premier League."
The addition of record signing Mesut Ozil, the return of combative midfielder Mathieu Flamini and a young squad that is constantly improving has renewed hopes that Wenger can finally steer the club to a first trophy since the 2005 FA Cup.
Wenger, though, must feel a change in fortunate is also due if they are to win Europe's top club prize for the first time.
Arsenal have fallen at the first knockout round for the last three seasons after being drawn against Europe's finest.
Spanish giants Barcelona knocked them out in 2011 en route to winning the title while in the last edition they were dumped out at the same stage by eventual winners Bayern Munich after they faced the toughest of seeded teams.
Arsenal did win their Champions League group in the 2011-12 season and were seeded only to be paired with then Italian champions AC Milan who beat them 4-3 on aggregate.
"We have now qualified for a 14th consecutive year for the last 16 and maybe number 14 will bring us a bit of luck," a hopeful Wenger said.