The batsman's England future hangs in the balance due to unrest in the dressing room after the 32-year-old admitted to sending 'derogatory' text messages about his teammates to friends within the South Africa squad.
"I think it's fair to say that his issues over being available for the entire IPL have changed his attitude," said Flower.
"I think that was the catalyst for a lot of the stuff. The IPL and the international fixtures in England are an area of conflict. And it will continue to be an area of conflict in the future."
Pietersen was not considered for the World Twenty20 squad as the ECB continue to deliberate the batsman's future.