The Brazilian defender was left out of the first-team squad for their 4-0 friendly win over Rot-Weiss Erfurt and instead had to play for the second string in a friendly match.
The accusations of being messed around by Bayern have since been removed from the internet, but not before the club's director of sport Christian Nerlinger spotted them, and he has vowed to investigate.
"Players should never be making such remarks, that is unfortunate," he told Bavarian television.
"Professionals must act responsibly on social network sites. I will only comment further when I have personally spoken to Breno."
Until the authenticity of the comments can be confirmed, Bayern are not jumping to any conclusions about a player they have supported through a difficult period recently.
Breno, 22, was arrested on suspicion of arson after his house in Munich burnt down late last year before being released on bail.