No one seems to know why 49ers defense is struggling this much

While the 49ers offense has undoubtedly been a key culprit in their three-game losing streak, the bigger concern for 49ers faithful seems to be the defense that has stopped… well, defending.

Perhaps the biggest concern: No one seems to be able to tell what exactly is going wrong, or how to fix it.

The 49ers defense had arguably its worst game of the season Sunday, allowing 31 points and 400 total yards in a loss to the Cincinnati Bengals. That effort came just a week after another bad showing, when the Minnesota Vikings had 452 yards of offense and scored 22 points to beat the Niners on Oct. 23.

On Sunday, the Niners were picked apart by Bengals quarterback Joe Burrow, who completed 28 of 32 passes for 283 yards and three touchdowns. He added six rushes for 43 yards for good measure. Burrow had been immobile for most of the first six weeks of the season because of a calf injury, but his sudden running prowess (after Cincinnati’s bye week) had Greg Papa, the 49ers’ play-by-play broadcaster and KNBR-AM midday host, befuddled.

“Their quarterback was completely healthy for the first time all year,” Papa said on KNBR’s “Papa and Lund” show Monday. “I don’t know how he got healthy, if he went to Canada to get stem cell or whatever the hell he did. I don’t know how you get healthy in the middle of the season except coming off the bye, but he did get healthier. … Yesterday, that was the full Joe Burrow.”

The 49ers were able to sack Burrow three times, but those would matter more if San Francisco was only getting beat through the air. But their run defense has faltered, too, as the Bengals ran for an average of nearly 5 yards per carry (134 rushing yards on 27 carries). It’s the second poor week in three games for the red and gold on the ground, after they allowed 160 yards on 34 carries in Cleveland in Week 6.

It’s clear that the defensive line is struggling, which led former 49ers safety and current NBC Sports Bay Area analyst Donte Whitner to call the front four “Velcro” in his weekly KNBR interview with “Papa and Lund” on Monday. 

“The offensive line is getting up to the second level very easily, you have guys backdooring, you have defensive ends who are penetrating way too far up-field on run plays,” Whitner said. “That’s not team football.”

That may be why there is continued scrutiny on defensive coordinator Steve Wilks, who was under the microscope for a failed blitz call last week in Minnesota. Linebacker Fred Warner defended the defense boss, saying after the game Sunday that “players win games, not coaches.” He added of Wilks: “I think he’s done a great job. There’s going to be ebbs and flows in the season, especially with a new defensive coordinator.”

Still, there’s a call for something to change with Wilks. 49ers radio color commentator Tim Ryan said Monday on KNBR’s “Murph and Mac” morning show that he wants Wilks to stop calling the defense from the press box and come down to the sidelines, like prior defensive coordinators Robert Saleh and DeMeco Ryans.

“I would not mind seeing the coordinator on the sideline,” Ryan said. “The only reason I say that is the coordinators do a good job from the box — Dan Quinn comes to mind right away in Dallas — but this defense, just go back to the Minnesota game, and some of the things they were trying to do different and weren’t working from a defensive structure standpoint in terms of the coverage.”

For his part, head coach Kyle Shanahan took some of the pressure off Wilks after Sunday’s game. 

“This isn’t on any one coach or any one side of the ball. We haven’t scored over 20 points here in three weeks, too,” Shanahan said Sunday. “So, I think our defense needs to do better. I think our offense needs to do better. I think our team needs to do better. And when I say our team, I mean every single player in there and I mean every single coach.” 

If the 49ers want to make a trade, they have less than 24 hours till the NFL trade deadline at 1 p.m. on Tuesday to do it. Shanahan downplayed the need for a roster change, saying, “I do believe we have the answers in our building. I believe we have good players. I believe we have good coaches. It’s up to me to get them to do better.”

With their bye week coming up, the 49ers will have two long weeks to try and figure out what’s been going wrong — and try to save their season in the process.