For one thing, the 49ers are simply a way better team. They're obviously a lot better coached, and were able to get focused. Their defense was able to get stops, and their offense didn't panic. It was able to get very focused and make plays. They also benefited from the opposing coach's stupidity. Dan Campbell does deserve some credit for building the Lions into a highly competitive team. However, his philosophy of "always be aggressive no matter what the context" hurts his team. He left 6 points (two field goals) on the field, then ended up losing by 3 points. A good coach knows, based on context, when to be aggressive and when to play it close to the vest. His "always aggressive" approach is reckless, and the 49ers made him pay for it. I can guarantee you that Coach Shanahan knew of Campbell's weakness and had a plan to exploit it.
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The 49ers didn't let the Lions' lead rattle them. They had confidence that they're a good team that could fight its way back. We saw that in their game against the Packers as well. Many Cowboys players get visibly rattled; Dak's not the only one. That tells me that our coaching is not up to snuff. These very scenarios should be covered in training camp. No matter how good you get, you won't be able to just steamroll over everyone. The league has too much talent distributed with parity for that. It makes me wonder if the Cowboys started to believe the media hype when they were blowing lesser teams out in the regular season.