Kyle Shanahan wants 49ers to clean up mistakes from Week 1 win

SANTA CLARA - Midway through the 49ers' crucial, gritty, hard-fought road victory over the Tampa Bay Buccaneers, Kyle Shanahan berated Jimmy Garoppolo on the sideline.

Shanahan's face was tomato red. Garoppolo shook his head apparently to indicate he thought he did nothing wrong. Shanahan raised his eyebrows in disagreement and read Garoppolo the riot act.

Garoppolo had just forced an incomplete pass to a covered wide receiver on third-and-12 from the Bucs' 18-yard line when George Kittle was wide open for a touchdown in the middle of the field. Garoppolo didn't see him. Earlier in the game, Garoppolo telegraphed a throw to the sideline, a throw which Bucs cornerback Vernon Hargreaves intercepted and returned for a touchdown.

Garoppolo ultimately played well enough to beat the Bucs. But his mistakes revealed Shanahan's frustration about the 49ers' sloppy performance, and the challenges they will face if they don't clean up their act.

Here are the five biggest challenges the 49ers must address before Sunday's game in Cincinnati:

1. Missed reads.

After the Bucs game, Shanahan came to the interview room and explained why he was so frustrated during the game. “There was some things out there that we missed, which I think made it a much tighter game than it needed to be.”

Shanahan was talking about two offensive plays in particular. Both came in the red zone. One was the incomplete pass to Bourne when Kittle was open. The other occurred early in the first quarter. This time, Bourne was open over the middle for a touchdown, and Garoppolo forced an incomplete pass to Kittle instead.

On both plays, the Buccaneers defense used Cover 4 (four deep zone defenders, three underneath zone defenders), and Shanahan called the perfect plays to beat it. Cover 4 is vulnerable in the deep middle of the field, between the safeties. Shanahan attacked that window with post routes and seam routes - Football 101. If Garoppolo had read the coverage correctly, he would have known to pass over the middle. That's probably why Shanahan yelled at him.

“He made a couple of good throws,” Shanahan said, “but Jimmy and everyone else, including myself, needs to get a lot more consistent.”

2. Bad decisions

The 49ers have the makings of a dominant defense. Meaning they don't need Garoppolo to take risks and make plays. They need him to manage games and not throw interceptions.

In nine starts with the 49ers, Garoppolo has thrown nine picks. And on Sunday, he threw a pick-six. Dropped back, stared down his target and floated a bad pass across the field.

After the game, Shanahan explained what Garoppolo should do different next time: “Don't throw it. The cornerback was flat footed. He made a great break on the ball. That's why it's scary to throw (across) the field. Jimmy's got the arm, but that corner teed off on it and made a risky gamble and made us pay. That's one you've got to learn from.”

Garoppolo made the same mistake last season against the Detroit Lions. He dropped back, stared down his target, floated a bad pass across the field, the Lions made the potential game-winning interception, but it didn't count because the Lions committed a penalty away from the play. Lucky Jimmy.

When will Garoppolo learn? If he doesn't learn soon, the 49ers could bench him, according to Mike Silver of NFL Network. “He had rough moments in the preseason,” Silver said recently on television. “He's coming back from the knee injury. Guys, keep an eye on this. If Garoppolo struggles, or continues to struggle, and they're either losing or he's not playing well or both, I don't think it's that far-fetched that they could make a quarterback switch earlier than some people might imagine.”

Keep both eyes on this.

3. Penalties

The 49ers had the worst red-zone offense in the NFL last season. On Sunday, the red-zone issues persisted. The 49ers came away with no touchdowns during their three trips inside the Bucs' 20-yard line, largely because of penalties.

First, Kyle Juszczyk committed offensive pass interference, which negated an eight-yard touchdown catch by Kittle. Next, Richie James Jr. committed holding and negated a 15-yard touchdown run by Raheem Mostert. Finally, Mike McGlinchey lined up incorrectly and negated another touchdown catch by Kittle.

“We got 21 points called back from penalties,” Shanahan said. “Gave the Bucs a number of free first downs off penalties. Just a lot of self-inflicted wounds we weren't proud of.”

The 49ers committed 11 penalties. Some of them were aggressive in nature, such as holding and unnecessary roughness. Those are understandable. But five were pre-snap penalties, which aren't aggressive - they're sloppy. Those are the ones to eliminate.

4. Injuries

The 49ers have dealt with them since Shanahan became the head coach in 2017.

The 49ers lost running back Jerick McKinnon for the season before the Bucs game. His replacement, Tevin Coleman, whom the 49ers signed this offseason, suffered a high-ankle sprain during the first quarter and didn't play in the second half.

“I'm pretty sure he's not going to be around this week,” Shanahan said. “We'll take it week-to-week after that.”

In addition, Nick Bosa, the 49ers' first-round pick, also has a high-ankle sprain - he suffered it during training camp and played through it Week 1. But it's sore again, and it forced him to miss Wednesday's practice.

“High-ankle sprains usually linger throughout the year,” Shanahan said. “When you get into games, usually you do stuff (to the injury) again. Hopefully, you can recover by Sunday.”

Meaning two of the 49ers' biggest additions this offseason - Bosa and Coleman - could feel the effects of their injuries all season. Depth is crucial at running back and defensive line.

Fortunately for the 49ers, those are two of their deepest positions. Matt Breida and Raheem Mostert can replace Tevin Coleman, and Arik Armstead and Ronald Blair can replace Bosa if necessary.

5. Interior run defense

The 49ers' defense carried the team to victory, but the interior run defense was vulnerable during the second half. Upcoming opponents will see that when they study the coaches' video. Buccaneers running back Ronald Jones averaged a whopping 7.4 yards per carry after halftime, and he mostly ran right through the middle of the 49ers' defensive line.

Part of the 49ers' problem was the absence of linebacker Kwon Alexander. He got ejected in the first quarter for using his helmet to hit Bucs quarterback Jameis Winston. Alexander will return Sunday and improve the run defense.

But another part of the problem was stud defensive tackle Deforest Buckner, arguably the best player on the team. Yes, Buckner. The 49ers' new “Wide 9” alignment isolates him, because the defensive ends line up so far outside the offensive tackles. During run plays, the Bucs consistently blocked Buckner with two offensive linemen and created holes the size of craters.

The 49ers have to find ways to plug those gaping holes. They could send blitzers into the area Buckner vacates when the double team moves him, or they could simply ditch the Wide 9 against teams that run the ball well.

Decisions, decisions.