McCaffrey has not practiced since August 8, leading to unfounded speculation that the running back's absence could also be related to a contract dispute.
"I think people make a lot of assumptions, and that would be one that they're wrong on," Shanahan said.
The 49ers head coach also commented on McCaffrey's potential return timeline.
"I think if it wasn't Christian, and we were in a game week, I think he would play today," Shanahan said.
When asked if McCaffrey's setback was related to his previous calf or Achilles issues, Shanahan responded, "No, just some tightness. He'll get sensitive if I say where."
Nick Bosa injury update
Shanahan also provided an update on defensive end Nick Bosa, who has not practiced since August 3 due to soreness and tendinitis in his surgically repaired knee following his ACL injury.
"He's making a lot of progress," Shanahan said. "He has a lot less irritation, soreness, and tendinitis—whatever you want to call it—than he had last week. So we think he's going in the right direction, and we see him similar to Christian."
49ers wide receiver injury updates
Wide receiver Mike Evans' practice ended early on Tuesday. He exited the field to have his left foot/ankle wrapped and iced. The good news is that Evans was seen shortly afterward observing the remainder of practice, with his foot/ankle no longer wrapped—though his quad had an ice pack on it.
Remember, Evans missed training camp time due to a quad strain.
"They just said he has some tightness, so we were just being smart, taking him out," Shanahan said. "I don't think it's anything worse, so we'll see when we get in there, but nothing that I'm worried about right now."
Shanahan also commented on the status of wide receiver Christian Kirk, who has missed significant time due to a calf strain.
"That's been unfortunate for him because he had the same thing in OTAs, so he missed that," Shanahan said. "And he hasn't been ready to go. He did it the first practice, before we even got to team periods, so I know he's been extremely frustrated with it.
"We love the guy so far, but hopefully, he can have some better luck going forward here so he gets some reps out here."
Mykel Williams a long shot for Week 1
Defensive lineman Mykel Williams continues to work his way back from the ACL injury that shortened his rookie 2025 campaign. While the 49ers aren't dismissing the possibility that he could be ready for the start of the season, they believe a later return timeline is more likely.
"He's further away than those other guys you just asked about, but we do think he's close," Shanahan said. "I do think Week 1 would be a long shot, but we haven't ruled it out yet. But he's progressing very well."
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