The easiest way to understand this is that even if the models were accurate, the financial crisis would still have occurred. So blaming the models would be confusing cause and effect regardless of whether you think the models were wrong intentionally or unintentionally.
That said, I didn't read the book so I have nothing to say about whether or not Nate Silver actually does this.
The models certainly contributed. (Note: I have read this far in the book.)
The modeling error in question was independence; that is, if you have five mortgages, each with a 5% change of default, then these can be packaged up as an AAA security as follows: you only lose your money if all five default. A bit riskier package is that you lose if 4/5 default. And so on, each with different returns.
If they are independent, the p(default) = 1/20^5. If they are dependent, it is 1/20. Now multiple mortgage pool size by a 100 or 1,000 or 10,000 (?) and see how far off the estimated risk is. :)
Now combine this with a 30-to-1 leverage when buying these "AAA" securities.
(This was quite a good problem to work through with my daughter to see what that little "independence" assumption means. :)
His main point here was that modeling failures are typically due to out-of-sample conditions; when the housing bubble broke, the markets were might more tightly coupled across the country than the modelers assumed. While they could have seen this kind of dependence if they looked to Japan, there was no such precedence in the US in recent history.
This is a beginner mistake which I have a hard time believing the entire mortgage market failed to spot.
My personal belief is that they knew of the flaw of the models but did not care since their personal incentives were more profitable if the model was not fixed.
As Michael Lewis found in the Big Short. His Liar's Poker (from the 80's) explains the mentality. As he says in the former, he thought the latter would be the be-all end-all.
But the kids in Business School would constantly write him and ask him for new ways to rig the game.
That said, I didn't read the book so I have nothing to say about whether or not Nate Silver actually does this.