The pair had a tense relationship for much of last season, which culminated in Muller questioning his future at the end of the campaign.
Asked if he was surprised by Ancelotti's decision, the striker replied: "Yes, I do not know exactly what qualities the coach wants. Mine are seemingly not 100% was he's asking!"
New Bayern sports chief Hasan Salihamidzic was asked if he was unhappy with Muller's comments and replied: "No! We have a lot of games this season and know what we have in Thomas."