KANSAS CITY, Mo. — Kyle Shanahan was watching as Jimmy Garoppolo scrambled toward the 49ers sideline and, rather than safely duck out of bounds, stepped back to his right and took a wicked shot from Steven Nelson.

At first, the San Francisco coach thought his quarterback had sustained a concussion.

Turns out it may have been a season-ending knee injury.

Garoppolo’s left knee buckled just before the Chiefs cornerback delivered a shoulder-to-shoulder blow, and that was the reason he went down so hard. Garoppolo was on the turf for a couple minutes before he was helped to his feet and eventually carted off late in a 38-27 loss to Kansas City.

“We fear an ACL,” Shanahan said afterward. “We’ll find out more tomorrow.”

That’s bad news for the banged-up 49ers (1-2), who already lost top running back Jerick McKinnon to a season-ending knee injury.

Backup quarterback C.J. Beathard said he spoke to Garoppolo briefly in the trainer’s room, and what little of their exchange he was willing to repeat made it quite clear the 49ers’ franchise quarterback – who signed a five-year, $137.5 million extension in February – expects his season to be over.

“I told him I’ll be praying for him and I love him and he just told me to lead these guys,” Beathard said. “I’ve never been in that situation with something possibly that serious. I can only imagine how tough it is for him this early in the season.”

PACKERS: Linebacker Clay Matthews does not understand why he was flagged – yet again – for roughing the passer, this time while sacking Washington’s Alex Smith on Sunday.

Matthews think it’s an indication that the NFL is “getting soft.”

Even Smith wasn’t quite sure about the call that came with 48 seconds left in Washington’s 31-17 victory. Nor did other players and coaches. Matthews broke free into the backfield, grabbed Smith with both arms and took down the QB in a seemingly straightforward manner.

“When you’re tackling a guy from the front, you’re going to land on him. I understand the spirit of the rule. When you have a hit like that, that’s a football play. I even went up to Alex Smith after the game and asked him: What do you think? What can I do differently?” Matthews said.

“That’s a football play. I hit him from the front, got my head across, wrapped up. I’ve never heard of anybody tackling somebody without any hands. When he gives himself up as soon as you hit him, your body weight is going to go on him.”

There are sure to be more questions and more debate around the NFL about what constitutes a penalty on such plays.

Matthews immediately put his arms up and slapped himself in the helmet as the flag was thrown. Packers Coach Mike McCarthy threw down a play-calling sheet and argued with two officials about the call, even chasing one along the sideline.

“I think Clay did exactly what he’s supposed to do there,” McCarthy said. “He hit him with his shoulder. He was coming full speed off of a block. He braced himself. So I was fine with what Clay did.”

In Green Bay’s 29-29 tie against the Minnesota Vikings last week, a potential win-sealing interception for the Packers was wiped out by a roughing call on Matthews when he hit Kirk Cousins.

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