The problem is that with such an uncertain performance, Bayern could once again miss out on the Champions League title. Last season, Bayern also looked great from the start (and in the Bundesliga too) - they scored a lot of goals but also conceded a lot. The pattern is repeating this season, with Bayern risking get an inconvenient/lucky Champions League opponent and be knockouted early on.
Domestic league form doesn't mean a club will not perform well in the Champion's League. A good example is Real Madrid. Last season was actually one of the few seasons where Real Madrid performed well both in the UCL and la Liga.
Bayern Munich will turn things around in an already weak looking local league as usual.
There is no doubt that Bayern will change the situation in the local league. But the problem is that they want to win the Champions League. To do this, you have to be much stronger than just "strong enough to win the Bundesliga". Bayern concede a lot of goals and started scoring a little - it is obvious that if this is not corrected, any strong opponent can knock them out of the Champions League playoffs.