Van Gorder's ineptitude easily swung the two regular season losses that way. With even a mediocre defensive coordinator, that should have been an undefeated regular season.
The thing that saved Van Gorder's job that year was the fact that Jaylon Smith was on that field, and that helped compensate for Van Gorder's piss poor playcalling. Who else would run a cover three scheme against a run-heavy team (Stanford)?