The most significant concern surrounds left guard Aaron Banks. The team fears he suffered an injury that could likely end his season.
"They thought it was most likely an MCL," Shanahan said.
Banks is scheduled to become an unrestricted free agent after the season.
Linebacker Dre Greenlaw, playing in just his second game since recovering from the Achilles injury he suffered in February, was forced to leave early. Greenlaw sustained a right calf injury during the first drive and did not return.
When asked if the injury is reason for concern, Shanahan said, "It can be. It was one of the first four plays—I know it was the first drive. He felt tightness in the calf. So, once that happened, we shut him down. We'll see if he pulled it or anything, but we didn't test it anymore after that."
Shanahan added that the team didn't even consider letting Greenlaw return.
"Once we heard about his calf, we shut him down," Shanahan reiterated.
Teammates express concern
Greenlaw's teammates voiced their concerns after the game, hinting that the linebacker may have returned from his Achilles injury too soon.
"I felt for him today," defensive end Nick Bosa said. "He really wanted to play out the rest of this year. He's an incredible player, and I think, sometimes with him, we need to protect him from himself because he'll play through anything.
"And sometimes, when you go through an injury like that, and it's not ready, I think the best thing for him would be to take it as slow as he can."
Linebacker Fred Warner also shared his thoughts.
"I love going out there to battle with him, but at the end of the day, it's about saving Dre from himself sometimes, too," Warner said. "He's coming back from a major injury, and everybody looks at the last game (against the Rams) and how great he was, and it's like, 'That's not normal.'
"He's dealing with something significant, so we gotta just protect him from himself sometimes."
When asked about Greenlaw's demeanor after the game, Warner shared that the injured linebacker was visibly upset.
"He's down," Warner said. "I mean, Dre's built the right way. He wants to be out there. He wants to help us win games. And that's my brother. At the end of the day, like I said, we gotta hold him back from hurting himself more."
Additional injuries
Other injuries from the game included tackle Jaylon Moore, who suffered a quad injury, and linebacker Dee Winters, who exited with a chest injury. Neither player returned.
The 49ers will look to regroup as they prepare for a Week 17 matchup against the Detroit Lions at Levi's Stadium.
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