Ancelotti was sacked on Thursday following a comprehensive 3-0 defeat to former club Paris Saint-Germain in the Champions League, the latest chapter in an underwhelming start to the campaign at home and abroad.
In announcing the decision, Bayern CEO Karl-Heinz Rummenigge claimed Ancelotti's dismissal was due to the team's performances failing to meet expectations.
But Hoeness indicated that dressing-room fractions played a key part in the manager's downfall.
"There were five players against Ancelotti," Hoeness told Westfalenpost.
"It was impossible to get out of that."
Star trio Robert Lewandowski, Thomas Muller and Arjen Robben have all voiced their discontent at various stages of the season, with the latter refusing to back Ancelotti after the defeat in Paris.
When questioned on Thursday, the 58-year-old former AC Milan, Real Madrid and Chelsea boss told reporters: "I don't want to speak but I will be writing a statement."
Former France defender Willy Sagnol has been installed as manager on an interim basis.