I've watched almost any Bayern game the past 5-6 years, if I had to single out elementary weaknesses, here would be my favourites:
Width: Bayern is using the whole pitch to combine, up and down, left to right and while they are relatively safe on the ball, they don't plan for possession losses. When they're attacking, then they are too offensive minded, sending way too many men forward followed by a high defense line. It barely matters that Boateng is pretty fast, he has to defend while running backwards, that's an adventure for any defender. And when they are in build up, then they havetheir players spread out a lot, leaving big holes open in defense. i don't know why Guardiola is still playing this system, he has players more than capable of linking up well with each other with fewer players needed for that.
However, please refrain from any sort of quick assumptions. Yes, they are vulnerable to high pressure and counters, but it's not like this is some sort of ultimate antidote. What do you think are the clubs in Bundesliga doing for years already? It's not like Bayern just played the first match of their club career vs Juventus. I'm pretty sure that a well-known Bundesliga coach is capable of keeping up mentally with a random INternet-Forum user suggesting tactics. Chances are: He has already tried that.
Crossing: When Bayern is in desperate need of a goal, and the opponent would jsut shut down and park the bus, then Bayern will most likely cross the fuck out of you. This is as much of a weakness as it is a strength actually. It's a lottery, You can't consecutively defend it, because you won't be able to shut down their crosses. All you can do is basically clear it out again. And that mostly works, but not everytime. Bayern needs just 1 player to finally hit it with his head, and there's fire. They will either score on you, or concede on the counter. I could imagine this to be unpleasant for Barca though, because they would want to outplay Bayern completely and stay in full control of whats happening. But crosses are unpredictable and it's an aspect in the game where Neymar, Messi, Iniesta etc are of little help.
Defending a lead: I think this is a struggle everyone can relate to. If you're 2-0 up and you're opponent scores the 1-2, then the equalizer just isn't far away. Nervousity is bitch.