49ers know they must cut down on penalties

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Jim Harbaugh has publicly complained about officiating more than once since he joined the 49ers in 2011, but on Monday, the head coach of the NFL’s most-penalized team declined to blame outsiders for a two-game losing streak.

“We never point any finger of blame or make excuses in terms of the officiating,” Harbaugh said.

This, of course, led to an obvious question: Um, what about Anquan Boldin, coach?

Several players complained about officiating after the 49ers were flagged nine times for 107 yards in a 23-14 loss at Arizona on Sunday and Boldin served as their angry spokesman.

The 33-year-old wide receiver said officials needs to be “held accountable” for their calls, which he termed “crap that costs us another game.” The 49ers were flagged for four personal fouls — two on hits to quarterback Drew Stanton — in the final 22 minutes. Boldin was flagged for head-butting safety Tony Jefferson in the fourth quarter, a penalty he acknowledged was justified.

“Look at the amount of calls we got, the times we got them,” Boldin said. “The personal fouls, hitting quarterback. I mean, guys taking perfect shots at the quarterback. Both of those, I mean, if you look at it, it’s unbelievable.”

Harbaugh, who memorably complained about what he deemed to be too-physical coverage from the Seahawks’ cornerbacks in 2012, was asked about Boldin’s complaints.

“There’s frustration,” Harbaugh said. “It can appear that something is working against you. I term it the football gods. … And you work to fix it.”

After Boldin’s head-butt penalty Sunday, Harbaugh spoke with his livid wide receiver on the sideline. It was quite a contrast from January: In a divisional-playoff win at Carolina, it was Boldin who restrained an out-of-control Harbaugh after the head coach received a 15-yard penalty for running onto the field to protest a call.

Niners coach Jim Harbaugh said officials are not to blame for his team’s problems. Niners coach Jim Harbaugh said officials are not to blame for his team’s problems. Photo: Christian Petersen, Staff / Getty Images Photo: Christian Petersen, Staff / Getty Images Image 1 of / 1 Caption Close 49ers know they must cut down on penalties 1 / 1 Back to Gallery

“Anquan was telling me to stay off the field,” Harbaugh said at the time. “He said, 'Coach, we can’t have that. Get off the field.’ And he was right.”

On Monday, Harbaugh was asked if he’d now counsel Boldin about his no-excuses philosophy when it comes to officiating. Harbaugh said he’ll address it and noted Boldin was speaking shortly after a frustrating loss.

“I think cooler heads will prevail,” Harbaugh said.

Perhaps the 49ers will keep their cool in the locker room, but what about on the field? They have been outscored 38-3 in the second half of back-to-back losses and have been flagged 12 times for 119 yards in those four quarters.

Linebacker Dan Skuta, who was flagged for unnecessary roughness for hitting Stanton as he was sliding at the end of a scramble, acknowledged the steady stream of flags has, at times, gotten in his head.

“A little bit because you start to feel you don’t have it in your hand anymore at some point,” Skuta said. “What do you do? It gets tough.”

The 49ers lead the NFL with 36 penalties, five more than second-place Pittsburgh. They are tied with the Rams for second in penalty yards (305).

The 49ers, who have eight starters who are at least 30 years old, should be able to withstand in-game adversity, including penalties called against them they perceive to be bogus.

Is Harbaugh pleased with how his team has kept its poise in response to the parade of the penalties? He didn’t answer the question directly, but acknowledged things must change before the Eagles (3-0) arrive.

“We’ve got a week to get it fixed,” he said. “Sunday at 1 o’clock, that’s the challenge for our ballclub.”

Injury report: A bright spot in Sunday’s painful loss: no significant injuries.

Defensive lineman Ray McDonald dislocated his finger in the fourth quarter, but it won’t prevent him from playing against the Eagles. It’s not clear if tight end Vernon Davis (knee, ankle) will return after he missed a game for the second time since 2007.

“Optimistic,” Harbaugh said. “Very hopeful that he’ll be able to play Sunday.”

Eric Branch is a San Francisco Chronicle staff writer. E-mail: ebranch@sfchronicle.com Twitter: @Eric_Branch