SANTA CLARA -- Sometimes Jim Harbaugh reveals more by what he doesn't say and the direct questions he most strenuously declines to answer.

Maybe it's intentional and just the natural Harbaugh-media jujitsu.

Or maybe it's the only way he can act when the questions hit a 49ers hot spot and Harbaugh gets that look on his face.

Which brings us to Monday: Harbaugh was asked about specific criticism of quarterback Colin Kaepernick's ability to go through multiple reads in the wake of Sunday's offensive flat-line 10-9 loss to Carolina.

And Harbaugh got that look on his face. He didn't want to answer the question, but he also had a point to make, and that probably told us more than anything else.

Almost exactly one year since Alex Smith suffered the concussion that put Kaepernick in as the 49ers quarterback, there is a QB/passing game issue here. But maybe not the one everybody thinks.

"I understand what you're doing and what you're trying to do -- glomming on to somebody's opinion that, you know, thinks whatever they think," Harbaugh said, probably referring to Trent Dilfer's less-than-flattering analysis of Kaepernick on ESPN.

"The main thing is that we'll look at it and talk about it with our players and see the areas we can improve.

"Just dissecting it as a unit, we had too many negative plays in the game. Too many negative plays, loss of yardage plays, penalties, sack, turnover ... that we've got to get better at. We didn't do a good enough job."

Again, it's interesting to think about what Harbaugh didn't say here.

He didn't go into an impassioned defense of Kaepernick's QB vision, he didn't say the analysis is completely silly, and he didn't say everything is going beautifully with the 49ers offense.

Knowing Harbaugh, I'm also sure he wasn't implicitly knocking Kaepernick, because Harbaugh always backs up his players in public and private and because I'm sure he's 100 percent convinced that Kaepernick is the right guy.

But between the lines, it's clear that the 49ers passing offense is gummed up and that Harbaugh and offensive coordinator Greg Roman are working through some things with it (and some injuries).

Also, Kaepernick, after his almost entirely fantastic 2012 campaign, is having some issues in 2013 finding his receivers, who are having even more issues getting open.

This doesn't mean Kaepernick has hit a wall or that Harbaugh and Roman aren't sure what to do with him.

I think if any of that were at all the case, Harbaugh's current responses to Kaepernick questions would be haughtier and more defensive -- the way he used to respond to A.J. Jenkins questions.

No, I just think that Harbaugh knows Kaepernick is still going through some growing pains only 19 games into his NFL starting career, and Harbaugh isn't here to either baby him or blame him.

How does Harbaugh evaluate Kaepernick's performance this season? Here's how: He won't, not really.

"There's been tremendous play by our quarterback, there's been tremendous play by our line, there's been tremendous play by our backs, the tight ends, receivers," Harbaugh said. "That's all taken place and occurred.

"There's been great play-calling, there's been exceptional work. And everybody involved with it is working harder than you can imagine to get it to be the kind of winning edge that, kind of, we need it to be. Championship type of football."

Right now, the 49ers have a title-level defense and an offense that has dropped them to NFC wild-card kind of football.

The 49ers are positioned as the NFC's sixth seed (the second wild card), tied at 6-3 with No. 5 Carolina. Winning the NFC West -- with Seattle 21/2 games ahead and with a home-loaded schedule to close the season -- seems far-fetched.

But there's a strong history of lower-seeded teams getting hot in January and winning the Super Bowl -- Baltimore won last season as a No. 4, the New York Giants won the season previous as a No. 4, and Green Bay won the season before that as a No. 6.

The 49ers have been beaten by the lower-seeded but hotter team the last two seasons; can they be the hot team this season?

If Kaepernick and the pass offense get past this stage, maybe once Michael Crabtree gets back in the lineup, they probably can.

It's not all on Kaepernick's shoulders, and Harbaugh doesn't want it on his QB's shoulders.

But you can also tell that Harbaugh is thinking about this, grinding through the scenarios and probably wondering if the rest of the season will tip one way or the other because of this.

Read Tim Kawakami's Talking Points blog at blogs.mercurynews.com/kawakami. Contact him at tkawakami@mercurynews.com.