CSN Bay Area

Programming note: Watch Monday’s 49ers press conference with head coach Jim Harbaugh on CSN Bay Area and streaming live online here at 12 p.m.

What you need to know: The game was not lost with the controversial penalty called on Ahmad Brooks’ self-described “bear hug” against Drew Brees that negated a late-game turnover.

At that point, the 49ers still held a three-point lead with three minutes to play.

The 49ers’ got the ball back with 2:06 remaining after the score was tied. But all facets of the team were ultimately responsible for the 49ers’ 23-20 loss to the New Orleans Saints even after referee Tony Corrente’s controversial call went against them.

[RELATED: Controversial penalty erases defining moment for 49ers' defense]

Let’s start with the offense. Again, the offense was stagnate. Colin Kaepernick and the passing game managed just 115 net yards. Kaepernick completed 17 of 31 passes for 127 yards with two touchdowns and one interception.

The Saints exploited an injury to left guard Mike Iupati to call for a stunt on that side of the line. New Orleans pass-rushers Junior Galette and Keyunta Dawson broke through against fill-in guard Adam Snyder and left tackle Joe Staley to record a 9-yard sack.

On a third-and-19 from the 11, Kaepernick was knocked out of bounds to stop the clock as he came up 3 yards short of a first down on a scramble.

“I think we made it difficult on ourselves at times and we didn’t execute like we should have,” Kaepernick said. “And then we just didn’t make the plays when we had a chance.”

Andy Lee came through with a 48-yard punt with enough hang time to force Saints return man Darren Sproles to signal for a fair catch at the New Orleans 25. However, 49ers gunner Kassim Osgood appeared to look up to follow the flight of the ball when Sproles had his hand in the air. Osgood tackled Sproles shortly after he made the catch, resulting in a 15-yard penalty for fair catch interference.

“I will take the whole weight of the loss on my one mistake,” Osgood wrote on Twitter after the game.

But the defense had a chance to bail him out and force overtime.

Brees found wide receiver Marques Colston with a step on 49ers cornerback Carlos Rogers on a crossing pattern for a 20-yard gain. Then, Saints tight end Jimmy Graham, who appeared to get away with a false start, made a 12-yard reception to set up Garrett Hartley’s 31-yard field goal as time expired.

The 49ers (6-4) have lost back-to-back games for the second time this season. And it was their second disheartening loss in the Superdome in 10 ½ months. In February, the 49ers lost to the Baltimore Ravens, 34-31, in Super Bowl XLVII.

“I thought that they played their hearts out and kept fighting,” 49ers coach Jim Harbaugh said. “It’s a tough loss, but we’ll keep playing, playing hard, playing fast and playing tough. That is what our guys did. I thought they played their guts out.”

Mangini’s role: Former NFL head coach Eric Mangini has a nebulous role as the 49ers’ senior offensive consultant. But Harbaugh revealed some of Mangini’s responsibilities after Sunday’s loss.

The 49ers made two ill-advised replay challenges in the first half. Both plays were obviously ruled correctly on the field. The failed challenges cost the 49ers two timeouts and the 49ers were unable to make any challenges in the second half.

Without seeing a replay, the 49ers challenged whether Saints quarterback Drew Brees threw an illegal forward pass beyond the line of scrimmage. He clearly did not. And the second challenge was that Jon Baldwin made a catch in the end zone for a touchdown. Baldwin clearly did not have control of the ball after going to the ground out of bounds – a necessity for the play to be ruled a touchdown.

“I was talking to Eric,” Harbaugh said.

Harbaugh admitted that they did not see a replay before challenging the Brees pass. And on the second challenge of Baldwin’s play, it was hazy, too.

“We knew he was in,” Harbaugh said. “We knew there was a question whether the ball was bobbling and we decided to challenge it,” Harbaugh said.

Too much on plate? The 49ers continued to struggle with getting the ball snapped on time. The 49ers took a timeout on offense before their third play of the game. Kaepernick tried to take another timeout later in the first half, but the 49ers already exhausted timeouts because of the two failed challenges. That sequence resulted in a delay-of-game penalty.

When asked why the 49ers continue to struggle in that area, Kaepernick pointed to the number of play calls that he receives in the huddle and the pre-snap adjustments that he must relay to his teammates at the line of scrimmage after taking a look at the opposition’s defense.

“We have a lot on our plate, as far as what we’re trying to get done,” Kaepernick said.

When asked if 49ers offensive coordinator Greg Roman and Harbaugh must simplify things in the future, Kaepernick answered, “That’s not my call.”

Power-based offense: The 49ers thought they could overpower the Saints defense, which came into the game ranked No. 23 in the NFL against the run. The 49ers’ tight ends of Vernon Davis (56), Vance McDonald (38) and Derek Carrier (3) played a combined 97 snaps. In comparison, the team’s wide receivers (Anquan Boldin 49, Mario Manningham 27, Jon Baldwin 16 and Osgood 2) combined for just 94 snaps.

Moreover, the 49ers relied heavily on fullback Bruce Miller, too. He was on the field for 33 of the 49ers’ 57 offensive plays. The strategy did not work, as the 49ers managed just 81 yards rushing on 22 attempts. Gore was held to 48 yards on 13 carries.

Gore played 47 snaps, while Kendall Hunter (7) and LaMichael James (4) saw limited action. Reserve running back Anthony Dixon did not play a snap of offense, and he expressed his discontent on Twitter after the game.

“It (just) sucks to have major skill and not allowed to show it,” Dixon wrote. He added, “I know I'm a threat (and) I know my game is ready to dominate at the highest level.” On the season, Dixon has 35 yards and two touchdowns rushing on 15 attempts.

Wright’s debut: Cornerback Eric Wright, a seven-year veteran, made his first appearance in a 49ers’ uniform and played in an NFL game for the first time in a year. The 49ers opened the way for him to get onto the field last week with the release of cornerback Perrish Cox. And in his first game, Wright was forced into a significant role after starting cornerback Tarell Brown left the game due to a ribs injury.

Wright played 31 defensive snaps as a third cornerback after Brown exited late in the second quarter. Tramaine Brock, normally the team’s third cornerback, played 54 of the 49ers’ 69 defensive plays after taking over for Brown.

"In retrospect, I haven't played in a game in a year, but at the same time, I have a lot of experience," Wright told the Bay Area News Group. "Mentally, I'm very comfortable. Physically, it's coming to me.”

Injury report: Mike Iupati sustained a left knee injury when he was hit from the side when Gore was tackled into him in the third quarter. Afterward, Iupati had a brace on his knee and left the locker room on crutches. Harbaugh said he did not have an official update.

Tarell Brown was in extreme discomfort as he left the locker room. He appeared to sustain a ribs injury when he had ahold of running back Pierre Thomas near the goal line. Fullback Jed Collins’ knee struck Brown in the back as he entered the fray to attempt to block for Thomas.

Through Gore’s hands: Gore averaged 50 receptions a season from 2006 to 2010, but he has not been much of a factor catching passes out of the backfield since the arrival of Harbaugh and his staff. On Sunday, Gore let a big-play opportunity slip through his hands.

Gore dropped a pass in the middle of the fourth quarter down the left sideline that could’ve gone for big yards as Kaepernick escaped the rush and found Gore uncovered.

“I got to make that play,” Gore said. “I’m a better player than that. I just dropped it. We would’ve won the game.”

Quote of the day: ”I think we are, but we still have six more to go. We can still finish the season 12-4.”
--Kaepernick on whether he is surprised the 49ers have lost four games

Looking ahead: Wide receiver Michael Crabtree did not practice last week, so it seems unlikely he will be available for the 49ers’ game next Monday night against Washington. Crabtree remains on the reserve/physically-unable-to-perform list after undergoing surgery in May to repair a torn right Achilles. The game against Washington is vital to the 49ers’ playoff hopes. Carolina (6-3) plays the New England Patriots on Monday night. The Panthers are in second place in the NFC South behind the Saints (8-2) and are in line to be the top NFC wild-card team. The 49ers are one of three non-division leaders with 6-4 records, including the Arizona Cardinals. The 49ers can write off a third consecutive NFC West title, as the Seattle Seahawks (10-1) own a 3 ½-game lead on San Francisco.