The 49ers were taken to task in the first half by the Los Angeles Rams on Sunday.

Through the opening three drives, the Rams scored two touchdowns, a field goal, and racked up 196 total yards. San Francisco’s defense was playing glaringly soft coverage, and allowed Matthew Stafford, Puka Nacua and Tutu Atwell to dice them up. Kyren Williams was moving the chains on the ground.

Adjustments were begging to be made, and defensive coordinator Steve Wilks seemed to oblige.

In the second half, the 49ers had a couple interceptions as they started to pressure Stafford more regularly. The Rams’ run game disappeared, with Williams rushing five times for 12 yards.

Aside from Sean McVay’s hilarious bad-beat drive to end the game, the defense was stifling.

But it wasn’t a dominant defensive performance on the whole.

It asked questions of the play-calling, scheme, and whether this defense actually has quite a bit more it needs to figure out before being deemed elite.

Fred Warner discussed the issues after the game.

“In the first half, that run game kept them ahead of the sticks a lot,” Warner said. “They were taking what we were given them. We had to tighten things up in the back end and try and make it a little bit harder on Stafford… I think we were trying to relate to the backend that we needed to tighten things up.”

Nick Bosa said the 49ers “made some adjustments” to the front seven by adding run pressures, which he believed were effective.

It sounded and looked quite a bit like there was a disconnect between the secondary and the front seven.

On tape, it’s evident how basic the 49ers’ coverage was in the first half. There was a heavy dose of straight-up Cover-2, as supported by Tashaun Gipson Sr. and Talanoa Hufanga having the lowest and third-lowest (respectively) target rates in the NFL. They’re sitting deep and when the 49ers are getting attacked, it’s been underneath.

The Rams have success with quick patterns and a quarterback who delivers the ball rapidly. It shouldn’t have been a surprise.

While the second half was unquestionably successful, it was a bit head-scratching as to why it took so long for San Francisco to make adjustments.

In 2019, the 49ers won their first of now nine-straight regular season games against the Rams because of an adjustment Robert Saleh made. The Rams — then in the LA Coliseum — ran the ball down San Francisco’s throat for seven plays, 56 yards and a touchdown.

Saleh grabbed a tablet, talked to defensive line coach Kris Kocurek and made an adjustment that netted a rare podium performance — deemed worthwhile by Kyle Shanahan — for a defensive coordinator.

The 49ers got a pair of goal-line stops against the Rams and silenced them for the remainder. Los Angeles had 109 yards for the rest of the day and went 0-for-9 on third downs and 0-for-4 on fourth downs.

Wilks let things ride on Sunday.

He told reporters on Tuesday that he prefers to keep things relatively simple and get a feel for the game. He said they adjusted in the second half, when the defense allowing 164 yards over seven drives (including a meaningless 50-yard drive to a field goal to end the game.):

I think you get a feel throughout the course of the game, and I think you saw that the second half and the adjustments that we made when we came out. With our defensive line, I try to allow those guys to settle in and go play. I try not to do a lot, but it turned into a game that Stafford was getting rid of the ball quickly.

So, you didn’t really see the effect of what we are capable of doing up front because they didn’t have an opportunity to do that. So, I had to adjust to be able to give those guys time. And the only way you can give them time is to get stickier in coverage on the backend.

Wilks said the defense clearly has room for improvement, and admitted they’ll have to use disguises to make life tougher for quarterbacks, especially experienced ones like Stafford.

So why not employ that philosophy last Sunday? That’s what former 49ers corner Donte Whitner wondered.

He was harsh, saying on KNBR this week that he didn’t see the 49ers adjust at all defensively. The Rams simply made mistakes, Whitner argued:

Whitner pointed out this play in particular, where Fred Warner and Charvarius Ward should have been given the option to switch assignments. Instead, Warner, who was inside, took the vertical route towards the sideline and Ward took the crossing route. They nearly collided in coverage and Puka Nacua went for a 20-yard gain:

They even avoided a walk-in touchdown for Nacua on this busted coverage with Tashaun Gipson Sr.:

Wilks is a specialist in the defensive backfield, and that’s where the 49ers struggled. Is this a cause for panic?

Not yet. It’s September, when a lot of truly awful football is played. If this keeps up into the winter, some alarm bells might be ringing.

But for now, this seems to be more of an indicator of an adjustment period with this defense. When Wilks was brought in, it was with the explicit understanding that he’d keep the same structure intact.

When Saleh made that adjustment after the opening drive in 2019, had been running his system for two years. This is Wilks’ second week against a resurgent Rams offense of surprisingly good Madden computer-generated players.

To his credit, he’s already added five-man fronts, slotting Javon Hargrave between Javon Kinlaw and Arik Armstead like Hargrave had in Philadelphia. That’s been immediately successful, with Hargrave beating the center nearly every snap.

But for the most part, Wilks seems like he’s going to be patient, and might need to correct some fundamental issues on the backend before he gets consistently creative in his coverages.

In the locker room Tuesday, Warner acknowledged there are issues that need amending, but reflected Wilks’ tenor, saying “that’s a gradual process.”

It might sound a little odd coming from a defense that’s been elite for the past half decade, but with a new defensive coordinator and quite a few new faces in the secondary, this thing will likely take time to hit the right gear.