Brock Purdy’s toe injury isn’t the only headache for the 49ers’ quarterback room. Mac Jones aggravated a summer PCL sprain during their 16-15 win over the Cardinals on Sunday, battled through it, but threw a costly pick. The head coach wasn’t fully convinced by his performance.

The injury did affect Jones’ performance in one big moment. He threw an interception during the game, something he wished hadn’t happened. After the game, coach Kyle Shanahan addressed that blunder directly. “I know there’s a couple that he’d love to take back, have back. I thought his pick was just a bad play.”

Yet, Shanahan also had some praise for Jones.

“I thought he did some really good things,” the head coach said. The quarterback ended the day 27-of-41 for 284 yards and a touchdown. On the final drive, he completed five passes for 59 yards, setting up Eddy Pineiro’s 35-yard game-winning field goal. Those plays showed Jones’ poise under pressure and his ability to make the key throws when it mattered most for the 49ers.

Still, Jones’ health remains the bigger concern.

The injury appeared late in the third quarter after a hit from a couple of Cardinals’ defensive linemen. He got up limping and struggled on a handoff later in the drive. By the next 49ers’ possession, Jones was wearing a brace on his left knee. During the post-game, Shanahan gave an update but kept it cautious.

“On the drive, he hurt it in the red zone, when the one we went for it on fourth and goal from the two, and didn’t get it.” Beyond that, no new details. While this could turn into a serious issue for the 49ers, Shanahan is also juggling another big injury concern.

Kyle Shanahan’s concern over his defensive end

Nick Bosa didn’t even make it past the first quarter against the Cardinals. The 49ers’ star defensive lineman went down with what looked like a knee injury. Fans at Levi’s Stadium held their breath as he limped off the field.

After the game, Kyle Shanahan shared some relief. Bosa avoided an ACL tear, which would have kept him out for weeks. Still, the head coach admitted there are questions ahead of Week 4.

“There is concern because of how he heels,” Shanahan said. “But the initial physical test did not indicate that. Hopefully, we’ll have some good news tomorrow.” The 49ers need their pass rusher at full strength, and Shanahan isn’t taking any chances. So what actually happened?

Bosa went down late in the second quarter after a brutal double-team by two Cardinals offensive linemen. On the final play of the drive, he grabbed his knee and made his way to the sideline, wincing with every step. Fans and teammates could see immediately that this was serious, and it cast a shadow over the rest of the game for the Silver and Red.

On the sidelines, the preliminary exam wasn’t enough.

The medical staff quickly moved him to the medical tent for a full evaluation. He was initially questionable, but later ruled out.

Even though he was walking, his left knee was wrapped in ice, signaling the seriousness of the injury. Now it’s a waiting game to see how Shanahan and the 49ers manage the injuries and keep their team ready for the road ahead.