Never mind, it was in the article:

A perfect example of the lack of chemistry was McCaffrey’s 7-yard touchdown catch. Inside linebacker Blake Martinez and safety Josh Jones had tight end Greg Olsen and McCaffrey, who ran complementary routes. Both Martinez and Jones went with Olsen and McCaffrey was left wide open.

“We practice it through the week,” inside linebackers coach Scott McCurley lamented with pain in his voice. “It was a top concept in what we do and we didn’t get it executed between he and Josh in there.
This kind of thing is why I suspect its the assistant coaches as much as Capers. But are their skills lacking or does Capers assume they know more than they can teach? Is the scheme so complex that a rookie and 2nd year player cannot remember it even if well taught during the week?

Those are the answers you need.