Shanahan explains why he’s frustrated with the 49ers third down struggles and lack of second half points

49ers head coach Kyle Shanahan came off exasperated when discussing the third down play on both sides of the ball between his 49ers and the Atlanta Falcons. San Francisco finished the game 3-for-8 on third down, while the Falcons converted nine of their 14 conversions.

It didn’t help that Atlanta gained 37 yards on 3rd & 2, converted a 3rd & 12, and scored from the seven-yard line on 3rd & 3. Nevertheless, DeMeco Ryans’ bunch remains a top-10 unit in preventing third-down conversions.

But for as good as this team has been defensively, third down has been their Achilles heel. Per RBDSM, the 49ers are 19th in defensive success rate on third and fourth down and 23rd in EPA per play allowed.

You can expect this type of variance when you live and die by the blitz on late downs. Monday, Shanahan mentioned one 3rd & 13 play where the 49ers' defense had a free runner but could not bring Falcons quarterback Marcus Mariota down. Additionally, both passing touchdowns through the air were surrendered by slot cornerback Samuel Womack playing on the outside against Kyle Pitts and reserve safety George Odum.

Here’s more from Shanahan on the Falcons wearing the defense down:

“They wore us down. We knew that would be tough, that’s what they try to do to everybody and I think at times we did decent, but they got in way too many third-and-shorts and when we had our opportunity at some third-and-longs, I thought we kind of blew it. And when that happens and that team stays out on the field, especially when the offense turns it over three times, that doesn’t shock me at all.”

What’s shocking is how inept the offense looks on third downs. The best offenses forgo third down and win on early downs. Unfortunately, that hasn’t been the case for the Niners.

Does this team have a discipline issue?

When you look at the 49ers' stats on a per-drive basis, they’re struggling to move the ball, which is why they’re hovering around league average on third down. A team with George Kittle, Deebo Samuel, and Brandon Aiyuk ranks 19th in yards per drive, 23rd in points and plays per drive, and 22nd in drive success rate, per Football Outsiders.

The talent is there, as is the play-caller. Injuries are an issue for every team as we approach the halfway point of the season. When you watched the 49ers on offense in Week 6, you wouldn’t have known there were injury issues. So, what gives?

Playing from behind the chains doesn’t help. San Francisco is the 9th-most penalized team from a per-play standpoint.

In the 4th quarter, when the score was 28-14, and the Niners had an opportunity to score, a 39-yard reception was negated by a Jake Brendel holding call. So, instead of the ball at the Falcons' 38-yard line with 7:27 to play, it comes back to the 49ers' 13. The offense didn’t reach Atlanta’s 38 for another three minutes.

These examples are ubiquitous when you look through the play-by-play data from this past week and the entire season. There’s a discipline issue on offense. A lack of attention to detail for the most essential part of the game: fundamentals.

Second half struggles

If it’s not a penalty, it’s a drop. As someone who believes referencing drops are overrated, the Niners had two unforgivable ones on Sunday. First, if Ray-Ray McCloud catches a pass, the 49ers are in the red zone with a chance to tie the game with just over a minute off the clock in the third quarter. Then, Charlie Woerner drops a pass that would’ve taken the Niners into Atlanta territory. On back-to-back possessions, potential points turn into punts.

We’d be lying if we acted like there weren’t these miscues on offense every game. There isn’t one person to blame. Later this morning, Akash will tell you that the head coach needs to look in the mirror.

Per ESPN’s Nick Wagoner, the 49ers rank 27th in the NFL in points per second half and 27th in yards per play. That’s down 12 points from the first half and nearly two full yards in yards per play. That’s an issue.

So while we can look at the other side of the ball and chalk up the defensive issues to not winning on early downs, the 4.8 yards to go on third down were the seventh-shortest for a 49er opponent in Shanahan’s tenure, Jimmy Garoppolo and company have left plenty of meat on the bone as the game has gone along.

Don’t get me wrong; there is some noise in those numbers. Shanahan goes into a shell with a big lead. That’s been the case this season against the Panthers, Rams, and Seahawks. And for those clamoring for more sense of urgency from the offense when they were down two scores in the second half, it’s not how they operate.

Only four teams take more time off the clock in between plays than the Niners, per Football Outsiders. They are built to bleed the clock and wear the opponent down. So, when the script is flipped, Sunday’s second half is the product.

Last year, the 49ers were limited on offense. That was in large part due to Jimmy Garoppolo. That’s not the case this year. Jimmy isn’t turning the ball over, as evidenced by San Francisco ranking third in interceptions per drive. Yes, he’s fresh off two interceptions, but that’s ignoring context and his season as a whole.

What we saw Sunday from Brandon Aiyuk was top-10 receiver-esque. We know Deebo Samuel can run through the faces of multiple defenders in one play. There’s speed and physicality with a quarterback who is all of a sudden willing to throw the ball down the field. Common sense would tell you the 49ers will figure it out. But we’re six weeks in, and it hasn’t happened yet.

This team is tough to figure out. They’re a .500 ball club and, quite frankly, play like one. When you look at the three teams the 49ers lost to, they have a combined 4-11 record outside their games against the Niners.

Which means they’ll reel off three victories in a row against the Chiefs, Rams, and Chargers — three potential playoff teams. For the sake of their season, there might not be much of a choice for Shanahan and the 49ers.