San Francisco 49ers

49ers notes: Harbaugh says team must do better managing clock

Coach Jim Harbaugh said the 49ers must do a better job managing the clock one day after the team committed two delay-of-game penalties and ran out of timeouts with more than three minutes remaining.

“That’s something we have to keep addressing and stay on top of,” Harbaugh said Monday. “There were a few too many times when the play clock was ticking down close to zero. We’ve all got to do a better job getting back into the huddle, getting the plays in quickly and early, and managing the clock.”

It’s not surprising that the 49ers lead the league in delay-of-game penalties after four weeks. They had more than any other team last year, too.

In 2013, teams averaged 4.6 delay-of-game fouls over their 16-game seasons, according to the NFL. The 49ers had 11. The only other team that came close to that number was Tampa Bay, with nine. Three teams – the Panthers, Packers and Patriots – had one.

Through four games, the 49ers are on pace to top last year. Only one other team – Tampa Bay again – has three, and 11 teams have not been called for delay of game.

Harbaugh said the 49ers should have been given three delay-of-game calls Sunday. He wanted quarterback Colin Kaepernick to take the penalty after failing to induce the Eagles to jump offside on fourth and 2 in the second half. Instead, Kaepernick called timeout.

That left the 49ers with one timeout, which was used later on Harbaugh’s failed coach’s challenge. He’s 1-3 on challenges after going 2-9 last year.

Making history – The 49ers became the second team in NFL history to allow three touchdowns by the opponent’s defense or special teams and still win. The 2007 Cowboys beat Buffalo 25-24 despite the Bills’ two interception returns for touchdowns and a 103-yard kickoff return.

Harbaugh praised the 49ers’ defense and cited three players by name: safety Antoine Bethea, cornerback Perrish Cox and defensive end Justin Smith.

“I thought they did a great job, all 11, playing together,” Harbaugh said. “And that was really the theme.”

Injuries – Harbaugh had no update on tight end Vernon Davis or right offensive tackle Anthony Davis. Both left Sunday’s game and did not return.

Vernon Davis is believed to have suffered a back spasm. He said he was “fine” after the game, but he was walking gingerly.

Anthony Davis had an MRI on Monday on his knee after two players fell into him from behind. The knee was heavily wrapped Sunday evening, and Davis took weight off the joint with the help of crutches.

“I’d hate to comment on anything before it’s official,” Harbaugh said.

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