When asked if Mustapha's status for the Week 10 matchup was in jeopardy, Shanahan responded, "Yeah, it is. Hopefully, it won't be too big of a deal, but halfway through practice, his calf was bothering him, so we shut him down there."
Shanahan noted that he hadn't yet received further details on Mustapha's condition, acknowledging that additional tests would be necessary to assess the injury's severity.
"We'll find out more about it later today," Shanahan continued. "But hopefully, it's not too bad, but you really never know."
The 49ers recently signed veteran safety Tashaun Gipson to the practice squad. Last season, he started 16 games for the team.
Wide receivers Deebo Samuel and Jauan Jennings were also limited on Thursday. Samuel is dealing with rib and oblique injuries, while Jennings has missed the last two games due to a hip injury.
"They've had a good week," Shanahan said. "I expect them to be back."
You can listen to Shanahan's entire interview below.