There were no big flaws in Bayern's game that day. Arsenal sat deep specifically to shut down what muller and lewandowski could do, but I wouldn't call that exploiting. In fact Arsenal didn't really 'exploit' or target any aspect of Bayern's game (it's hard to find flaws against "top top class" teams anyway), they were just really well disciplined and played some really good high tempo counter attacks. The lay-low and counter attack was just a good gameplan, not really an 'exploit'.
But Bayern still mostly dominated and played really well. Arsenal's goal was mainly due a horror error by Neuer, he really should have caught or punched that. (Yes it's a set piece so anything can happen, but other than Walcott's header, Sanchez's chance and Giroud's late header from a corner, I don't really remember many more threatening set pieces, so Neuer should have really dealt with that, especially after the Walcott save.)
The only 'flaws' that Bayern had were that they didn't finish. Costa should have scored. Lewandowski should have scored maybe twice even though it was a quiet game for him by his standards. (Sanchez's mistake was what lead to Costa's chance on goal too.)
That last goal by Ozil was really just more of a case of Bellerin being a freak surprisingly right at the end of the match rather than Arsenal specifically exploiting anything. Arsenal was not high pressing (as a team) on that play, it was just a mistake (slow pass) combined with the incredible anticipation and speed from Bellerin (not to mention the desire to bolt into the box rather than jog to the corner flag).
In fact, you could clearly see throughout most of the match that Bayern was the one that kept wanting to target Nacho. Which was pretty weird because if they did their homework, they should have known how massively impressive Nacho has been recently.
> This has been slowly changing the past few seasons however.
And despite all of what I just said, I am acknowledging that Arsene isn't as 'old-fashioned' as he was maybe 5 years ago. Because that comment was more of an observation in general of the post-Highbury era, not literally the past few days when it's obvious that there's more to Arsene's game nowadays.
If you wanted to use a recent example anyway, the game against United would have been a much better example imo (league games is generally when you should be 'exploting' anyway, not in the cl, because you should be expecting anything in cl games, just because of the occasion). You could clearly see that Arsenal specifically targetted United's slow midfield by high pressing on them (Walcott's and Ozil's workrate was impressive). And they were basically one-twoing their way past Bastian "cannot run no more" Schweinsteiger the whole match.