Niners quarterback C.J. Beathard was at the center of those issues, throwing high to open receivers a few times, occasionally holding on to the ball too long and generally failing to get the ball down the field. But even as Beathard struggled, Shanahan resisted whatever urge might have existed to take a look at Jimmy Garoppolo. That's because, despite those issues, the offense's real problems were out of Beathard's control.
Sunday's 24-13 loss to the Seahawks had seemed like the right time for Garoppolo to start, but Shanahan repeatedly said he wouldn't put Garoppolo in until he believed he was in position to succeed or if an injury to Beathard forced his hand.
Turns out, that's exactly what happened.
Garoppolo finally made his 49ers debut with 1 minute, 7 seconds to play after Beathard suffered an injury on his 14th hit of the day. Garoppolo received a loud ovation as he entered, and promptly scrambled for 4 yards and completed two passes for 18 yards and a touchdown. It was a tantalizing debut that will surely raise the question of when Garoppolo will make his starting debut.
For most of Sunday's loss, Beathard rarely dropped back to pass without having a Seahawks defender in his face. Seattle hit Beathard 14 times, including three sacks, and he took a couple more on designed runs and scrambles. This game didn't look much like the first meeting between these teams so much as it did the Niners' loss to Philadelphia where Beathard left with more bumps and bruises than completions.
Now, Shanahan has a real decision to make as Garoppolo didn't get much of a sample size but showed he can get the job done. It wouldn't be a surprise if he makes his first start next week in Chicago, his hometown.
What it means: First, the Niners will have to wait another year to end Seattle's run of dominance against them. Sunday's loss was their ninth straight at the hands of the Seahawks and came in a game that seemed to be there for the taking. Otherwise, the 1-10 Niners don't have much to gain from this loss save for the fact they remain the only team other than Cleveland in position to contend for the No. 1 pick in the 2018 draft.
What the 49ers did well: The Niners defense was able to keep it close for about two and a half quarters. Were it not for an early interception deep in San Francisco territory, the Niners didn't allow a substantial drive until midway through the third quarter. The Seahawks found some success late to pull away, but the Niners' defense kept them in it more than the final score might indicate. On offense, there wasn't much to write home about, save for a little glimpse of second-half success on the ground. Kicker Robbie Gould made both of his field goal attempts in windy conditions.
What the 49ers didn't do well: Given how much the 49ers struggled offensively in the first meeting, it shouldn't be a surprise that similar issues popped up again Sunday. The lack of protection, the inability to pop many explosive plays and a costly interception were part of another rough offensive showing. And some of those offensive struggles began to show up late in the game as the defense was unable to continue to keep Seattle out of the end zone. In two full games against Seattle this season, the 49ers didn't score a touchdown until the last play of this game.
Fantasy fallout: Running back Carlos Hyde had nowhere to run in the first half, but the Niners stuck to the run and he did find a little room in the third quarter. Still, Hyde was unable to duplicate his strong outing from the teams' first meeting. He finished with 47 yards on 16 carries, adding another 21 yards on seven receptions.
Musical safeties: With rookie Adrian Colbert inactive because of a broken thumb, the 49ers started their fourth free safety in as many games Sunday. This time it was Antone Exum Jr. stepping in for Colbert. Previously, the Niners lost Jimmie Ward and Jaquiski Tartt to broken arms in back-to-back weeks. The 49ers hope Colbert will be able to return next week.
What's next: After spending a month at home, the Niners are back on the road starting next week with a trip to Chicago. It could be the Niners' best chance for a second win.