SANTA CLARA, Calif. — The 49ers came away from Sunday’s 13-10 home loss to the St. Louis Rams with more issues than points.

Coach Jim Harbaugh came to work Monday with one solution: “I really want to talk to my team.”

That, apparently, will happen Tuesday, after the players stop scratching their heads over one of the most puzzling games of the Harbaugh era.

Play-calling, the team’s new center, the offensive philosophy, Colin Kaepernick’s weaknesses, the offensive line in general, the quality of the coaching, the referees — pretty much everything was fair game for criticism in the wake of a defeat that dropped the 49ers three games behind the Arizona Cardinals in the NFC West.

Even given nearly a full 24 hours to watch film and determine answers, Harbaugh was unwilling to make any of them public Monday.

“It’s a tough loss whether you characterize it as some guys are frustrated or surprised or we didn’t get the job done,” Harbaugh assessed. “That’s on the men in the room. That’s us.”

According to Harbaugh, all the 49ers’ would be in the room Tuesday, discussing, as the coach put it, “where we’re at, what we can learn from what we did and where we’re going.”

Where the 49ers are going next is to New Orleans. And unless attitudes change between now and when the plane leaves at the end of the work week, they’ll be taking with them a star running back who’s confused about the club’s offensive identity and a standout offensive lineman who pretty much sized up his unit’s play Sunday in one word: dumb.

“We’ve got to just, as a team, come in Tuesday and make our mind up where we want to go,” observed 49ers running back Frank Gore, who didn’t score a touchdown for a fourth consecutive game. “We’ve just got to make our minds up, do what we feel we’re good at and go do it.”

Offensive tackle Joe Staley was a little more pointed.

“We have all the talent in the world, We’ve been doing some dumb stuff,” he said. “Penalties, dumb blocks, dumb technique and dumb schemes.”

Sounds like there’s a lot to talk about.

NOTES, QUOTES

–49ers coach Jim Harbaugh wasn’t talking about pretty much anything Monday, so it was no surprise he offered no insights into his views — both live and after watching film — of three controversial calls that all potentially cost his team points in Sunday’s 13-10 loss to the St. Louis Rams.

The first occurred on the final play of the first half, when Rams return man Tavon Austin caught Phil Dawson’s field goal attempt in the back of the end zone and attempted to run it out.

He got just onto the field of play before either: a) Getting pushed back into the end zone; or b) Retreating back into the end zone on his own and then getting tackled.

The referees ruled the former, resulting in a touchback, and it was upheld on replay. The latter would have meant a two-point safety for the 49ers.

The other two came in a three-play sequence in the final seconds of regulation.

First, 49ers quarterback Colin Kaepernick connected with wideout Michael Crabtree near the goal line. Crabtree cradled the ball at the line, but his momentum carried him back onto the field of play, where he hit the ground and struggled to retain possession before rolling out of bounds.

The ruling could have gone any number of ways, but the referees opted to give Crabtree possession at the 1-yard line, while allowing the clock to continue to run.

Again, a reversal on replay would have meant points (this time six), but after review, the play stood as called.

Two plays later, from that same spot at the 1, Kaepernick attempted to sneak in. He juggled the snap, then regained control while diving forward into the pile.

Kaepernick landed in the end zone, but did so without the ball. When the dust settled, it was in the hands of Rams linebacker James Laurinaitis with two seconds remaining.

The referees ruled a fumble, giving the Rams the ball on the 20 after a touchback. And for a third time, the ruling was upheld on review, denying the 49ers would could have been a game-winning touchdown.

Kaepernick insisted he’d cross the goal line with the ball in his hands.

Addressing the three calls in general, all Harbaugh would say was, “Would have seen it differently. That’s probably understandable.”

–The 49ers allowed eight sacks in the loss. In the middle of the mess was their new center, Marcus Martin.

The rookie had issues other than the sacks. He and Kaepernick missed clear connection on snaps on at least three occasions, including the direct snap that preceded the quarterback’s last-second fumble in the end zone.

Afterward, Martin, who was replacing injured Daniel Kilgore (leg surgery, out for the season), wanted to watch the game film before assessing his performance.

“I don’t know off the top of my head,” Martin responded when asked to identify mistakes he had made. “There were some mistakes made and we didn’t play good enough to win. So that’s one thing we’ve got to improve upon.”

–Not that it impacted the outcome of the game, but the 49ers’ problems began even before they took the field Sunday.

Running back Marcus Lattimore, who participated in regular-season practices last week for the first time in his season and a half with the club, did not show up for the game amid a report that he had decided to retire.

Lattimore, who suffered major injuries to both knees during his college career at South Carolina, had worked out Wednesday and Thursday, but then sat out Friday while working behind the scenes with the 49ers’ medical staff.

Contacted Monday, Lattimore’s agent, Michael Perrett, said his client in fact had not retired, but rather was weighing his options.

The 49ers have two more weeks before having to decide whether to place Lattimore on the 53-man active roster or place him on injured reserve and declare him out for the season.

REPORT CARD VS. RAMS

–PASSING OFFENSE: D-minus — The 49ers did more bad than good in the passing game in Sunday’s 13-10 home loss to the St. Louis Rams. Colin Kaepernick had decent numbers — 22 of 33 for 237 yards — but his lone touchdown pass was the result of good field position following an interception. Kaepernick was sacked eight times, resulting in 57 yards in losses and helping produce seven punts.

–RUSHING OFFENSE: F –

Here is the confidence level in the 49ers’ rushing game: With two chances to punch in a potential game-winning score from the Rams’ 1-yard line in the final seconds Sunday, the 49ers opted for a play-action fake and a quarterback sneak. One (the pass) failed. The other (the sneak) blew up in the 49ers’ face when Colin Kaepernick fumbled as he dove for the goal line. Star RB Frank Gore came away from the game questioning the 49ers’ offensive identity.

–PASSING DEFENSE: B-plus – The key play in the 49ers’ only touchdown-scoring drive was an interception by S Antoine Bethea. That was one of two interceptions the 49ers recorded in their 13-10 loss to the Rams. The 49ers’ pass defense was so effective, the Rams opted to run the ball more than they threw it even though their ground game wasn’t doing much, either. OLB Aaron Lynch had another big game, including a sack, and has played his way into a regular role even after OLB Aldon Smith returns from his suspension. The Rams’ only touchdown was the result of a blown coverage by a backup linebacker (Chris Borland).

–RUSHING DEFENSE: A – The Rams’ basically had two motivations to run the ball Sunday: 1) Because they couldn’t do much passing it; and 2) To keep the clock running in a surprisingly close game. They ran the ball 27 times and recorded only three first downs rushing. Bottom line: Wherever they tried to run, they ran into 49ers backup ILB Chris Borland, who recorded 18 tackles.

–SPECIAL TEAMS: C-minus – Dependable Andy Lee shanked a punt out of bounds to set up the Rams’ game-winning field goal on a busy day when he still was able to average 44.9 yards per attempt. And Phil Dawson’s only missed field goal nearly resulted in two points when the 49ers tackled Rams return man Tavon Austin in the end zone. It was ruled a touchback. The 49ers appeared to catch a break when Austin erroneously was ruled to have stepped out of bounds on a return for a touchdown. The play was negated anyway by offsetting penalties.

–COACHING: F – There was no doubt who did the better job of coaching in this one. Rams coach Jeff Fisher flooded the 49ers’ backfield with pass rushers, containing Colin Kaepernick and forcing him to make quick reads. Instead of countering with more runs, the 49ers seemed content to prove Fisher’s ploy would not work against their star quarterback. In fact, it did, leaving some 49ers questioning the play-calling.