Each side of the ball puts eleven men on the field. But the "whole" can be greater than the sum of the parts when everything is clicking. Conversely, when things are not clicking or gelling, the "whole" can be less than the sum of its parts.
My guess (purely speculative) is that the eleven men we put out on offense and on defense in the 49ers game rarely if ever have played together as a unit before that week. So they ended up being less than the sum of their parts. On the other hand, we've seen individuals here and there come in to spot injured starters (e.g., Littleton, some of the DB's) and do just great because they have quality guys around them to support them.
Either way, as of right now, I trust this coaching staff to make the team even better next year. No hand-wringing necessary.