NFL Network's Rebecca Haarlow is reporting that a source close to free-agent Alex Smith says that the quarterback is indeed upset over what occurred during the 49ers' pursuit of Peyton Manning. Smith feels that it was not about the contract or money, but it was about the loyalty.

The 49ers have said that the communication with Smith during this time has been good. The team has offered Smith a 3-year, $24 million deal with $10 million guaranteed. Miami is rumored to be interested in offering a multi-year deal, also for about $8 million a year.

NFL Network's Steve Mariucci still believes that San Francisco is the best landing spot for Smith. Including the playoffs, Smith led the 49ers to a 14-4 overall record in 2011, completing over 60% of his passes for 3,639 yards, 22 touchdowns and just 5 interceptions.

Smith is back in the Bay Area after a visit with the Miami Dolphins. However, there are no scheduled meetings with Smith.

This afternoon, head coach Jim Harbaugh was seen leaving the team's headquarters in Santa Clara. When Matt Barrows of the Sacramento Bee (@mattbarrows) was asked on Twitter if he had returned yet, he had this to say:

Still gone. Either patching things up w/ No. 11 or took a half day

This morning, Peyton Manning decided to sign with Denver over Tennessee or San Francisco.