Yet the head coach will now undoubtedly be frowning as he tries to put together a squad for Saturday's league clash with Werder Bremen.
The first major headache came during 'Der Klassiker' when Joshua Kimmich picked up an injury that will now rule him out of action until the turn of the year. Which is when we're also likely to next see Alphonso Davies back on the pitch for Bayern.
The second headache came this week, when Kimmich's presumptive back-up in midfield, Corentin Tolisso, picked up a muscle injury on international duty with France and was also ruled out of Saturday's game.
This means Flick will most likely have to turn to 32-year-old Javi Martinez to anchor his midfield, in only his third start of the season for Bayern.
Elsewhere the Bavarian giants should be back to relative full strength, with Tanguy Nianzou back in training and Niklas Sule picking up game time with the German national team and presumably fit enough to play on Saturday if called upon.