The 49ers activated McCaffrey from injured reserve on Saturday, intending for the star running back to make his 2024 season debut. He has been sidelined with Achilles tendinitis.
Meanwhile, Samuel has been dealing with rib and oblique injuries, limiting his participation in practice throughout the week.
"They've had a good week," Shanahan said of Samuel and wide receiver Jauan Jennings, who has missed the last two games. "I expect them to be back."
The 49ers enter Week 10 with a 4-4 record, aiming to secure their first back-to-back wins of the season.
The other 49ers listed as questionable are defensive end Nick Bosa (hip) and safety Malik Mustapha (calf). Offensively lineman Jon Feliciano (knee) was downgraded and ruled out. He remains on injured reserve.
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