But there is always a bright side.
One good thing about the injuries this season is that they have given other players opportunities to showcase themselves to the coaching staff. That bodes well for the 49ers when they get back key players next season.
"We found out about a lot of guys this year that we weren't sure about, and guys that I think can help us next year," Shanahan said Friday morning on KNBR. "I am excited about next year. I keep saying you get better or worse, and I know our team is going in the right direction, getting better. And I strongly expect us to have a record that shows that next year."
One position devastated by injuries is running back. The team lost starter Jerick McKinnon to a torn ACL a week before the start of the regular season. Matt Breida has been battling injury all season, has never seemed 100 percent, and will not play in the 49ers' finale on Sunday against the Los Angeles Rams. Raheem Mostert fractured his right forearm during a Week 9 victory over the Oakland Raiders.
Each of those players should be completely healthy next season, which could potentially create a dangerous running back group. You can even throw Jeff Wilson Jr., who has contributed well here late in the season, into the mix of competition.
"The guys have stepped it up well," Shanahan said. "It's been tough with injuries throughout the year, especially losing Jet (McKinnon) before the season started. But guys have stepped it up.
"What Breida has done this year, especially playing through the injuries. He's been hurt really since almost the Kansas City game, and we've never been able to fully get him back. I know it's been frustrating for him, and he won't be able to play this week. What he's done even at not 100 percent -- we know his ankle will heal this offseason, so he'll come back better next year.
"He didn't get to play much before he got hurt, but what Raheem Mostert did in what I think was about four games, we really used him as a back. He finished this year averaging over seven yards a carry (7.2), which is unheard of. And he ran real. He broke tackles. It wasn't just open runs. He broke some big tackles and showed that he's not just a special teams player. He can really help us out.
"Losing Jet at the beginning of the year was unfortunate, but we found some depth. Going into next year, we've got some more guys we can depend on."
You can listen to the entire interview with Shanahan below. He also discusses the mindset headed into Week 17, the defense's improvement in recent weeks, creating offseason competition, linebacker Elijah Lee, handling Rams defensive tackle Aaron Donald, and more.
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