SANTA CLARA, Calif. -- In the early minutes of the San Francisco 49ers' Friday practice, there was plenty for them to be optimistic about on the injury front.

Running back Christian McCaffrey (knee) and defensive lineman Arik Armstead (foot, ankle) were again participating in practice. Even receiver Deebo Samuel (quad) was in uniform and a helmet.

But that optimism was quickly tempered when left tackle Trent Williams slowly walked off the field and straight to the locker room before team drills began. Niners coach Kyle Shanahan said Williams is dealing with back spasms, which has put his status for Sunday against the Miami Dolphins in question.

"I'm not too concerned about it," Shanahan said. "I asked [offensive line coach] Chris [Foerster] if he was all right. He said it was just big guy problems ... You usually have them on game day, that's a big deal so he had them today. He'll spend the day resting and stuff. And we expect him to be all right."

Officially, the Niners are listing Williams as questionable for Sunday. If he is unable to play, the 49ers would likely turn to third-year tackle Colton McKivitz. McKivitz filled in for Williams in a Week 4 win against the Los Angeles Rams.

Questionable is the same designation the Niners gave Samuel, who was in uniform Friday but didn't do much in the practice, according to Shanahan. Samuel was listed as limited Wednesday and did not participate Thursday.

"There was no setback," Shanahan said. "When you have a deep thigh bruise, you kind of have an idea how it's going to be and it just hasn't been as good as we were expecting by now. We were expecting him to be able to go full by now but he wasn't able to so that's why there's some concern."

If Samuel is unable to play, the 49ers would turn to a group including Jauan Jennings and Ray-Ray McCloud to fill in.

In addition to Williams and Samuel, Niners guard Spencer Burford (ankle) and defensive lineman Charles Omenihu (knee) are also listed as questionable.

Meanwhile, for the second time this season, running back Elijah Mitchell has been placed on injured reserve, which means he must miss at least the next four games before he's eligible to return. Mitchell is expected to miss six to eight weeks with the sprained medical collateral ligament in his left knee he suffered in last week's win against the New Orleans Saints.

While San Francisco is facing those key injury questions, it will have two of its best players available.

McCaffrey and Armstead do not have an injury designation and are cleared to go. McCaffrey has been dealing with what the Niners called "knee irritation" this week and was held out of practice Wednesday. But he participated the past couple of days and indicated Thursday he'd be able to play against the Dolphins.

"I feel great," McCaffrey said.

Armstead's return has been much longer in the making. He's been dealing with injuries to both feet and ankles since Week 4. His return comes after missing the previous seven games. Shanahan noted Armstead has had a "good week" and "passed the eye test" for what the Niners wanted to see from him to return. "It's just good to see him, what he's battled through to get back," defensive coordinator DeMeco Ryans said.

"It's been a long road for him, so it's just good to have him back out," he added. "... If we get an All-Pro player who can help our defense that would be a huge lift for us, so I'm excited for Armstead and just him working his way back in."