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SANTA CLARA — Game management could be an ongoing issue for the 49ers’ inexperienced coaching staff this season, although head coach Kyle Shanahan did not question his game management at his Monday news conference.

On Sunday, two questionable coaching decisions may have cost the 49ers a win, or at least a tie, against the Cardinals. The 49ers lost 18-15. The first questionable decision came from rookie defensive coordinator Robert Saleh.

With 2:24 left in overtime, the Cardinals got the ball at the 49ers’ 25-yard line. Until that point in the game, the 49ers mostly were aggressive on defense, blitzing and hitting Cardinals quarterback Carson Palmer 16 times. When the 49ers blitzed, Palmer’s quarterback rating was 72.2.

But when the Cardinals got the ball in overtime, Saleh decided to change his defensive approach. He became passive. He called a soft, prevent defense and didn’t blitz for the first three plays. During that time, the Cardinals drove to the San Francisco 36 and put themselves in field-goal range.

“If you (blitz) too much,” Shanahan said, “that’s what gets them better looks down the field … It’s a fine line. You’ve got to mix stuff up. If you know they’re going to get 12 yards on a check down, obviously you go man (coverage) or pressure, one or the other, because those check downs aren’t there when you do that. But also, would they have gotten a go route at that time? You don’t know.”

Blitzing had been effective for the 49ers. Palmer averaged only 5.9 yards per pass attempt when the 49ers blitzed.

The second questionable decision came from Shanahan himself two plays later.

With 1:17 left in overtime, 49ers defensive tackle DeForest Buckner drew a holding penalty and sacked Palmer at the San Francisco 30-yard line. Had Shanahan declined the penalty, the Cardinals would have faced third-and-15 from the 49ers’ 30. But Shanahan accepted the penalty and gave the Cardinals second-and-20 from the 49ers’ 35.

Shanahan said he wanted to push the Cardinals out of field goal range, but the 5 yards he gained may not have made a difference to Cardinals kicker Phil Dawson, who had made a 50-yard field goal earlier in the game. Dawson crushed it.

The 49ers probably would have been better off declining the penalty and forcing the Cardinals to convert on third-and-15, instead of giving them an extra down which turned out to be disastrous.

Instead, 49ers safety Jimmie Ward committed pass interference and gave the Cardinals a first down. Two plays later, Palmer threw the game-winning touchdown pass to Larry Fitzgerald.

“I’ll second guess everything, but I feel good with what I thought at the time,” Shanahan said. “My thought process there was if you push them back a little bit more, you know that you’ll entice them into getting greedy, and we’ll play man coverage and come after them and we’ll have a chance to sack them. If we don’t have a sack, we’ll have a chance to get a holding call. Either one of those, now they’re out of field goal range, and now I think we can win the game.”

When Shanahan makes crucial game-management decisions, such as the one above, he consults with the Special Assistant to the General Manager, Ryan Cordell. Cordell has no NFL coaching experience, and graduated from Notre Dame in 2013 with a degree in business administration.

The 49ers will have to consider improving their game management when they face the Colts this Sunday.

NOTES

Reporters asked Shanahan on Monday if he will bench quarterback Brian Hoyer, and Shanahan was adamant that he will not. “When you lose three games by a total of eight points, I know we very easily could be 3-1. You don’t want to make drastic changes. There are lot of things that go into losing games — it’s never just one guy.”

Safety Eric Reid and linebacker Reuben Foster probably won’t play Sunday against the Colts. Shanahan is “a little more optimistic” they will play the following week against the Redskins.

Wide receiver Marquise Goodwin is in the league’s concussion protocol after suffering a concussion against the Cardinals.