The San Francisco 49ers fell victim to an upset in Week 4. Even with Brock Purdy returning to action from a turf toe injury, San Francisco was upset by the Jacksonville Jaguars at home. The loss ended the 49ers' bid to stay undefeated this season.

It was a close contest, as the Jaguars won by just five points over the 49ers. After the game, 49ers head coach Kyle Shanahan revealed what the refs told him about a crucial call in the game.  In the second quarter of the game, the Jaguars were pinned at their own nine-yard line. On second-and-12, two flags were thrown following an incomplete pass: offensive holding on the Jags, and a personal foul on 49ers cornerback Upton Stout.

After some discussion, the flag on Stout was picked up. As a result, the Jaguars had to replay the down with the line of scrimmage moved to the four-yard line. Except… the 49ers didn't want that to happen. Kyle Shanahan was looking to decline the penalty, putting the Jaguars in third-and-12 instead of second-and-17. However, since Shanahan called a timeout to talk to the referees, the enforced spot was upheld.

After the game, Shanahan revealed that the referees admitted to him that they made a mistake in not asking the 49ers about the penalty.

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“They told me they messed up,” Shanahan said at the press conference.

With the Jaguars pinned deep in their own territory, a third-down stop would have guaranteed a punt for Jacksonville. Instead, the 49ers gave up a two-yard gain on second down, and then a 28-yard gain from Travis Hunter to get them out of their own endzone. From there, Jacksonville drove all the way down the field for a touchdown.

The missed call wasn't the only reason the 49ers lost, of course: Purdy threw two interceptions in his first game back and lost a fumble. It was a brutal game all around for San Francisco. With the score being so close, though, one has to wonder what would have happened if the referees got that second-down call right.

The 49ers have other problems to worry about, other than a missed call. The injuries are starting to pile up, with Purdy potentially reaggravating his injury and Ricky Pearsall suffering an injury as well.