Colin Kaepernick was not injured. Sorry, that’s just me trying to list all the things that went well during Sunday night’s game. Here’s another: no 49er was struck by lightning.

The 49ers lost 29-3 in a game that would’ve seemed long even without the weather delay, and in certain ways this was a worse defeat than the 42-13 loss in Seattle back in December. But as Justin Smith said during the week leading up to this game, “That was last year.” This year, or at least on Sunday Night Football during Week 2 of the 2013 season, the 49ers lost badly. It was complete failure against an opponent they can’t stand, and it was one of those equal-opportunity losses where no one looked good.

Colin KaepernickI haven’t seen every game Kaepernick has played, but it’s probably safe to assume his passing statistics have never been worse than 13-for-28, 127 yards, three interceptions and a quarterback rating of 20.1. Football starts with quarterback play, and Kaepernick was unable to lead the team to a single touchdown. Can’t blame the noise, either.

Anquan Boldin, who was clutched, grabbed and probably scratched by Richard Sherman all evening, ended the game with 12 fewer catches and 201 fewer yards than he had a week ago. Vernon Davis caught three passes for only 20 yards and left with a hamstring injury that came on a long pass intercepted by Sherman. The 49ers couldn’t move the ball through the air, and besides a few long scampers by Kaepernick their ground game also struggled.

But we’ve only scratched the surface of this most recent beat-down administered by Seattle. The 49ers defense — while much better overall than the Kaepernick-led unit that only held the ball for 23 minutes — wasn’t anything special. At least, not compared to Seattle’s group, which held San Francisco to just 207 total yards and 12 first downs.

The 49ers also might have lost Ian Williams for the season with a broken ankle (on a legal cut block that sure looked dirty, both to those watching on TV and 49ers like Patrick Willis, who afterward said “hit like a man” in reference to that play). Eric Reid left the game with a concussion sustained while hitting Sidney Rice after a first down-converting catch across the middle. Ray McDonald also limped off the field, although the x-rays on his ankle were negative.

Seattle’s secondary is outstanding, and Kaepernick will have better days. The 49ers proved they can pass effectively a week ago, so now isn’t the time to cry about Michael Crabtree’s absence or how Anquan Boldin and Kyle Williams aren’t Roddy White and Julio Jones. But there are a couple of worrisome trends we’ve seen from these two games that the coaching staff absolutely must fix.

Where’s Frank?

No one minded 21 carries for 44 yards when Kaepernick threw for 400+ and Frank Gore provided so many fantastic blocks both in the pocket and in space against the Packers. However, 9 Gore carries for 16 yards means defeat for the 49ers more often than not. Kendall Hunter didn’t play much and only got one touch (a run that lost seven yards). For whatever reason, the best run-blocking unit from 2012 isn’t opening up holes in 2013. Whether that’s an aberration or changes might be coming (like Daniel Kilgore in for Jonathan Goodwin, for instance) remains to be seen. But if they can’t establish anything on the ground with Gore and/or Hunter on Sunday against Indianapolis, one of the team’s biggest strengths officially becomes a confusing, unsettling, totally unexpected weakness.

Penalties

The 49ers committed the seventh-most penalties last year — 109, an average of 6.8 per game. This season the 49ers have been penalized 23 times for 206 yards. Surprisingly, Tampa Bay has also committed 23 penalties for even more yardage (220), but that’s a team with a coach in Greg Schiano who might not last the entire season. The 49ers are committing all kinds of penalties, and on Sunday the relative stupidity shown during each seemed to grow as the game went on. So many flags stick out as moments that harmed the team, but none was worse than Aldon Smith’s personal foul for popping Breno Giacomini in the head after a 15-yard pass on 3rd-and-28. The 49ers were only down 12-3 at the time, but instead of the Seahawks attempting a 44-yard field goal they were able to score a touchdown three plays later to get a three-score lead early in the fourth quarter.

The season is by no means lost, and it feels silly to even write something like that after Week 2. If Reid passes his concussion tests, the 49ers won’t be faced with trying to cover the Colts’ receivers with a Whitner/Dahl safety tandem (which didn’t look so hot at times against Seattle). Glenn Dorsey, who sacked Russell Wilson once, may well be better than the still-unproven Williams. The 49ers still have time to rediscover how to use their running backs effectively and avoid getting flagged every five minutes.

But they don’t have that much time, not with games against the Colts, Rams, Texans and Cardinals looming. Jim Harbaugh often uses the phrase “humble hearts” as both a mantra and goal. The Seahawks humbled Kaepernick and the rest of the 49ers on Sunday night, and we’ll see in a week’s time whether that leads to a turning point or if the injuries and disciplinary issues will become a season-long theme.