Jim Harbaugh began to lose the good will of some players on the San Francisco 49ers when he was not honest with Alex Smith about his pursuit of Peyton Manning in 2012.

Smith specifically asked Harbaugh about the 49ers' interest in Manning and did not get an answer that matched the facts of the situation, in which Harbaugh flew to North Carolina to meet and work out Manning, the sources said.

As one team source told ESPN, "that was the first big sign to the players that they couldn't trust Jim."

49ers CEO Jed York tweeted his support of Harbaugh on Sunday afternoon.