Well, when you go from the #2 defense to the #26 in a year (and with an arguably better roster than the year before), and lose the big game when you are expected to win largely due to breakdowns on defense, that kind of thing is bound to happen.
EDIT: To clarify, because someone reached out to me via PM and correctly challenged me on those numbers, that was their rank in run defense specifically, so sorry if I wasn't clear. In overall defensive efficiency, I believe they slid from #1 to #12, and in DVOA, from #1 to #4. But I know run defense was a BIG issue for Shanahan, and that's what I was intending to hit on.