No. 1: Kyle Shanahan, 49ers had poor clock management late in fourth quarter
Maybe this one is slightly excusable. But, without doubt, the overwhelming thought when fullback Kyle Juszczyk scored a go-ahead touchdown with only 43 seconds remaining in regulation was that Aaron Rodgers and the Packers had far too much time left with the score 28-27.
Even with Green Bay having zero timeouts left.
The “excusable” part is partially explained by Kyle Shanahan in his postgame comments:
"We wanted to run it down. No one wants to give it back to Aaron Rodgers. We’re also not going to tell Juszczyk to not try to score. …Usually, check downs at best are about a 5-yard gain, but Juszczyk ran a hell of a check down and then ran over two people to score. We had three timeouts, but I’m not telling [Jimmy Garoppolo] to run it down yet. You want to get under 30 seconds and inside the 10-yard line. Then you can control it with your three timeouts. But the only other option would have been to tell Juszczyk not to score, which is something you wouldn’t do."
If Juszczyk had intentionally gone down shy of scoring, and the Niners didn’t ultimately score, that decision would have been unquestionably scrutinized. Yet San Francisco could have called for at least one more run play to get inside the 10-yard line, which would have put Shanahan in a position where he could have dictated the remaining flow of the clock, perhaps then leading to the Juszczyk score on the subsequent play.
Once Rodgers had barely enough time, this decision nevertheless came back to haunt Shanahan.