49ers Cruise Past Dolphins but Interior Run Defense Remains Shanahan's Concern

San Francisco beat Miami 35-13 on Sunday, yet the head coach's worry about defending runs between the tackles only grew during the win.

The San Francisco 49ers defeated the Miami Dolphins 35-13 on Sunday in Santa Clara, but the lopsided result did not resolve an issue that has been weighing on head coach Kyle Shanahan: defending runs up the middle. Fox analyst Daryl Johnston told viewers during the broadcast that Shanahan had flagged the between-the-tackles run game as a concern in a pregame production meeting.

Miami kept the game close early by exploiting that weakness. The Dolphins held the ball for more than 19 minutes in the first half, ran 28 plays in 49ers territory, and picked up 84 yards on 20 carries. Their opening three drives lasted nine, 17, and 12 plays, producing two field goals and a missed 51-yard attempt, leaving San Francisco ahead just 14-6 before pulling away.

Rookie defensive tackle CJ West, a 2025 fourth-round pick pressed into the starting lineup after Alfred Collins suffered a season-ending knee injury, has struggled. His Pro Football Focus run-defense grade of 26.4 is last among 135 interior defensive linemen with at least 15 run snaps. Against Miami, center Aaron Brewer and guard Kaden Proctor repeatedly moved him off his spot, including on consecutive second-quarter plays that ended with West on the ground.

Rookie James Thompson, an undrafted free agent with a 28.5 run-defense grade that ranks 131st at the position, left with a high ankle sprain in the third quarter and is expected to miss roughly four weeks. Gracen Halton, who made his first career start in the game, could be in line for a larger role after out-snapping West 63-49 over the first two games.

Offensively, the 49ers leaned on the bootleg concepts long associated with Shanahan's system. Brock Purdy rolled out frequently, scoring on a 2-yard run and connecting with George Kittle on a 26-yard gain, while San Francisco reached the end zone on its first five drives for the first time since at least 1991.