Yet now is not the time for the 49ers to panic. In fact, San Francisco should be far from worried despite all of the elements that surrounded their Week 2 struggles. In fact, the 49ers have a trend over the past three years of bad losses early on in the season.
San Francisco was able to bounce back with victories following each of the early-season losses and ultimately make deep playoff runs in both seasons. Thus, one loss is nothing to be afraid of.
Still, there are a number of concerns that San Francisco has to address. What happened with quarterback Colin Kaepernick last Sunday? Are injuries going to be a big concern for the team in 2013? Why has running back Frank Gore struggled thus far into 2013? Is the offensive line as good as it should be?
These questions and more lay at the heart of the 49ers preparations for their Week 3 matchup against the Indianapolis Colts.
The good news is that San Francisco is playing Indianapolis at home. The Colts are not on the same level as the Seahawks and home-field advantage will help the 49ers get back on track.
The bad news is that the following questions must be addressed and soon.
The Injury Factor
Injuries can plague the best of teams.
San Francisco has not been immune to such setbacks thus far into 2013. From wide receiver Michael Crabtree's Achilles injury during organized team activities (OTAs) through significant injuries suffered last Sunday, the 49ers will have to move forward without some key personnel.
Defensive tackle Ian Williams, defensive end Ray McDonald, rookie safety Eric Reid and tight end Vernon Davis all left the Sunday Night Football game against Seattle because of injury.
In Williams' case, his broken ankle is significant enough for him to land on injured reserve, and he'll miss the remainder of the season. It is a good thing that San Francisco signed defensive tackle Glenn Dorsey this offseason; hopefully he can perform up to expectations in the increased role.
What of the other injured players?
McDonald is one of the unsung heroes of the 49ers' front seven. Currently, he is listed as questionable for the Colts game, and his absence could spell trouble for San Francisco's defense.
The same goes for Reid, who missed the second half of Sunday's game with a concussion.
49ers defensive coordinator Vic Fangio spoke of the injury situation on the 49ers' flagship station KNBR 680 about the situation. As transcribed by Matt Barrows of The Sacramento Bee, Fangio stated:
I think [McDonald] is going to be ok, but again it's a fluid situation. His ankle is bothering him a little bit, but we'll see how it goes. But I think it's much like the Eric Reid situation. We really won't know until the end of the week.
If both of those guys are good to go, the situation should be okay against Indianapolis. But, as stated by ESPN columnist Bill Williamson, if the players cannot suit up Sunday, the situation becomes a concern. Safety Craig Dahl and defensive lineman Tony Jerod-Eddie are the backups to Reid and McDonald, respectively.
What of Vernon Davis? He tweaked his hamstring on Sunday and was removed late in the game.
Davis has already tweeted that he should be ready before the game versus the Colts.
Yet Barrows pointed out in an interview with KNBR Wednesday morning that players are often overly optimistic about the state of their own injuries. Barrows also noted that rushing Davis back onto the field could potentially result in a more aggravated injury.
That is something San Francisco can ill afford.
Yet it is likely that Davis, McDonald and Reid take the field on Sunday. Pending any setbacks, all three should be playing in Week 3, albeit with some relief. They will probably just be limited in practice.
The Offensive Line
San Francisco's offensive line is one of the bulwarks of the franchise, yet they did not show it against Seattle.
Pro Football Focus (subscription required) ranked tackle Joe Staley as the best run-blocker in the league last season. On Sunday, Staley had a minus-4.9 grade, according to PFF’s system. The rest of the line similarly struggled.
There are a couple of factors behind the OL's lack of production in Week 2. First, the crowd noise at Seattle's CenturyLink Field is an obvious handicap, and coping with such a distraction makes any offensive line's job precarious.
In addition, having little success on early downs forced the team into a number of 3rd-and-long situations. That coupled with the Seahawks corners shutting down San Francisco's receivers on the outside made pass-blocking a difficult task.
Lastly, and perhaps most importantly, the Seahawks' front seven simply outplayed the 49ers' offensive line. As relayed by Matt Maiocco of CSN Bay Area, head coach Jim Harbaugh spoke about what the line needs to do to start winning the battle up front:
There are things we’ll put our finger on, and try to make improvement—significant improvement—this week. That’s something that early the part of the season, you want to make the most of, identifying where you can get better, make improvements, and you want to see those improvements made.
The Colts' defensive front is not of the caliber of Seattle's, and San Francisco's offensive line will benefit from that downgrade in talent.
Is Frank Gore Slowing Down?
Running back Frank Gore has not gotten off to a good start in 2013.
In Week 1 against the Green Bay Packers, Gore rushed for a mere 44 yards on 21 attempts. Against Seattle last week, Gore fared worse, totaling only 16 yards on nine attempts. Thus far in 2013, Gore is averaging a mere 2.0 yards per carry.
Simply put, that needs to change.
Before the beginning of the season, I wrote an article outlining some of the legitimate concerns for San Francisco heading into the year. Gore slowing down was one of the topics touched upon. Not surprisingly, many readers felt that the 49ers' running game was not a worry. Two weeks into the regular season, perhaps such concern is warranted.
At 30 years old, it is safe to say that Gore is entering the final years of his storied NFL career. Yet his poor showing over the first two weeks cannot be entirely attributed to age alone.
In Week 1, the Packers did an excellent job of limiting the ground attack of San Francisco's run-first offense. That attention to stopping Gore allowed Kaepernick to throw for over 400 yards.
In Week 2, the Seahawks manhandled the 49ers offensive line and a big Seattle lead eventually dictated that San Francisco abandon the running game.
Kyle McLorg of Bay Area Sports Guy agrees that the lack of production cannot be placed upon Gore alone. He writes:
Could Gore be losing a step? Possibly. But the blocking hasn’t been there for him so far, and the tape is ample proof. Through two games, the best run blocking offensive line in the league has taken a big step back, and if it corrects itself, Gore’s ability to chunk defenses will correct itself as well.
Gore may not be the elite back he once was, but there are few reasons to doubt the production yet to come. As long as the offensive line improves over the course of this and subsequent weeks, Gore should be fine.
These have to stop.
Any fan who watched San Francisco's abysmal performance in Week 2 would note how undisciplined the 49ers were against Seattle.
Granted, I felt the officiating was not at its best during the game, and the referees were a little "flag happy" throughout. Even so, the 49ers have been downright atrocious when it comes to penalties this season.
As reported by Cam Inman of the San Jose Mercury News, San Francisco stands as the second-most penalized team in the league with 25 infractions for 206 yards. A slew of them came in the Seahawks game, during which the 49ers got penalized 12 times for 121 yards, the highest total since head coach Jim Harbaugh's arrival in 2011.
Sure, the crowd noise was partly to blame, but it certainly didn't account for all the sloppy play. It is a troubling trend that needs to be addressed soon.
I have always felt that penalties should be handled at the coaching level, and that coaches should bear much of the accountability in ensuring these things do not happen. Fangio expanded on that coaching responsibility, via Eric Branch of SFGate.com:
It’s frustrating because we made a point of it during the week that in a game like that in particular those things can happen and we’ve got to be able to walk away from it—not get a penalty called on our ourselves and put it in the hands of the officials. We’ve got to do a better job in that area as coaches of getting that point across, and as players of learning that point.
Even some of the players have felt they need to take accountability for their own actions. Both Davis and Patrick Willis have come out saying that things need to change.
If any team continues to stock up the penalties, just penalty after penalty, it can cost you the season if you do it every game. But we're not going to allow that to happen. We're better than that. It was just a game where we just acted instead of thinking.
What the 49ers need to do is simple. The penalties—especially unsportsmanlike flags—need to be limited. San Francisco does not need to be the least-penalized team in the league to ensure postseason success, but they need to be better.
Colin Kaepernick Rediscovering His Rhythm
In Week 1, Colin Kaepernick was stellar. In Week 2, that was not the case.
Against the Packers, Kaepernick was able to showcase a rapport with wide receiver Anquan Boldin. In Seattle, the Seahawks shut Boldin down, and Kaepernick struggled to find other targets.
Look at the statistics: 406 passing yards in Week 1 versus only 107 in Week 2. Kaepernick threw three touchdowns against the Packers but threw three interceptions against Seattle.
Despite the poor showing against Seattle, Harbaugh concluded that Kaepernick was San Francisco's best weapon:
There was good coverage. There was pressure at times. I thought, when we go back and look at the tape, Colin competed, was seeing the field, made plays, made the most amount of plays that we made on offense. He probably played the best—(was the) most productive person we had on offense. (via Matt Barrows of The Sacramento Bee)
If Kaepernick was the best in that particular game, it does not say much about the rest of the 49ers offense.
Even Kaepernick acknowledged the fact that he needs to do better. After the game, Kaepernick said via Anne M. Peterson of The Huffington Post, "We're not going to win games if I play like that."
The good news is that Kaepernick will not be facing an elite secondary in Week 3 and should be able to resume his chemistry with Boldin. In addition, a healthy Davis should also give Kaepernick another viable weapon on offense.
Barrows also mentioned on KNBR Wednesday morning that Kaepernick has historically been a slow starter in games, citing last season's Week 15 matchup against the New England Patriots as the only time the young quarterback has produced a touchdown on an opening drive.
Unfortunately, Kaepernick's slow start in Seattle was too much for San Francisco to overcome, as the Seahawks were eventually able to put the game away in the second half.
That sluggishness out of the gate should change against a less-than-stellar Indianapolis secondary that allowed 315 passing yards to Miami's Ryan Tannehill last week.
With that in mind, Kaepernick should be just fine moving forward. Hopefully his poor performance is behind him, and he will have learned from his mistakes. Expect Kaepernick to bounce back nicely against Indianapolis.
There are a number of notable concerns for the 49ers moving forward. Thankfully, San Francisco will return to the comforts of Candlestick Park and face a Colts team that is not on the same tier as the Seahawks.
If anything, the 49ers should be able to utilize the mistakes from Week 2 to their advantage, learn from them and then put that knowledge into practice.
While these questions are still burning and yet to be answered, San Francisco and its coaching staff have all the ability in the world to turn the negatives into positives.
The start of that recovery process should be revealed against the Colts.
All statistics, records and accolades courtesy of Pro-Football-Reference.com unless otherwise stated.
Peter Panacy is a featured columnist for Bleacher Report, covering the San Francisco 49ers. Follow him @PeterMcShots on Twitter.