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The 2 Biggest Questions 49ers Still Haven't Answered After Free Agency

These questions better be answered soon.
Sep 7, 2025; Seattle, Washington, USA; San Francisco 49ers general manager John Lynch, right, talks with head coach Kyle Shanahan during pregame warmups against the Seattle Seahawks at Lumen Field. Mandatory Credit: Joe Nicholson-Imagn Images
Sep 7, 2025; Seattle, Washington, USA; San Francisco 49ers general manager John Lynch, right, talks with head coach Kyle Shanahan during pregame warmups against the Seattle Seahawks at Lumen Field. Mandatory Credit: Joe Nicholson-Imagn Images | Joe Nicholson-Imagn Images

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It is undeniable that the San Francisco 49ers have done a mighty fine job in free agency. They addressed the positions they were desperate for and didn't break the bank.

However, as solid a free agency period as they had, they still have a couple of questions leftover that need to be answered, and it starts with the safety position.

How will they improve at safety?

Malik Mustaph
Nov 16, 2025; Glendale, Arizona, USA; San Francisco 49ers safety Malik Mustapha (6) reacts in the second half against the Arizona Cardinals at State Farm Stadium. Mandatory Credit: Joe Camporeale-Imagn Images | Joe Camporeale-Imagn Images

The 49ers have an enormous question mark at the safety position. Not a single player they have there is an adequate starter. Ji'Ayir Brown is who he is at this point, which is mediocre to average.

Malik Mustapha could rebound in 2026 after a disappointing sophomore season, but I wouldn't hold my breath. His strength is as a run defender, which he regressed massively at.

And he was already a liability in pass coverage. Marques Sigle flashed in several facets, but he gets lost when the ball is in the air with him as the designated target.

The 49ers need to add a safety. Someone who they can confidently point to as a true starter. That isn't on their roster, but it seems they believe so. Otherwise, they would've made a move.

Maybe defensive coordinator Raheem Morris is a fan of the current safeties, and that he can get more out of them. I guess we'll see if that is their plan after the NFL draft.

What is up with Trent Williams?

Trent William
Jan 11, 2026; Philadelphia, PA, USA; San Francisco 49ers offensive tackle Trent Williams (71) celebrates win against the Philadelphia Eagles in an NFC Wild Card Round game at Lincoln Financial Field. Mandatory Credit: Eric Hartline-Imagn Images | Eric Hartline-Imagn Images

After the safety position, the most important question the 49ers still have resides with Trent Williams. How is that going to shake out with his contract?

They didn't pick up his $10 million option bonus, which is bizarre that a team can simply pass on paying a player. It's just weird that even is in a contract, but I digress.

The 49ers could extend Williams, giving him the long-term security he desires, which includes guaranteed money. It's clearly what he wants. He pulled this stunt on them two years ago.

And he's going to continue to do so, as he's still playing at an elite level. Plus, the 49ers don't have his heir apparent on the roster. Until that happens, Williams has all of the leverage in the world.

I understand the 49ers' reluctance to shell out more money to Williams. He's old now, which means he can fall off a cliff with his performance at any moment. And he's not the most reliable player healthwise.

Still, the 49ers don't have any other recourse. They didn't sign a feasible replacement at left tackle in free agency, and relying on a rookie to replace him would be insane.

Williams will likely end up getting what he wants in the end. It's best if the 49ers oblige instead of continuing to draw out this unnecessary dilemma.

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Jose Luis Sanchez III
JOSE SANCHEZ

Jose Luis Sanchez III has covered the San Francisco 49ers daily for FanNation since 2019. He started off as the lead publisher for FanNation's All49ers, then switched positions to become the Deputy Editor in 2020. Sanchez writes, edits, and produces videos daily for All49ers. He also co-hosts a show on YouTube with All49ers lead publisher Grant Cohn weekly. Prior to FanNation, Sanchez started his writing career back in 2016 for the school newspaper at Skyline college where he covered all sports team in the Bay Area. Following that from 2017 to 2019, he found a role as a contributor for FanSided's news desk along with their site's Just Blog Baby covering the Las Vegas Raiders and Golden Gate Sports every professional Bay Area sports team. Atop all of that, he was able to graduate with a Bachelors degree in Communication Studies at San Francisco State University in 2020. Sanchez is committed to ensuring he delivers transparent analysis and straightforward opinions that resonates with readers to get them thinking.

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