I think we have to be careful to avoid hindsight bias when thinking of examples of this. For example, it is quite possible that Jews who chose not to leave Nazi Germany before Kristalnacht were in fact acting perfectly rationally. Certainly Weinberg makes a reasonable case that they were acting rationally in this essay (and yes, I realise that he has plenty of reasons to try to justify himself, but that doesn't change the fact that it's possible he made a sensible decision).
I don't disagree at all. Also, the millions of Jews in areas subject to Nazi control had an enormous variety of differing constraints and circumstances.
No matter what, in order to find an unambiguous example of "motivated skepticism with grave consequences" from history (rather than in the context of an academic experiment), Luke is going to have to do his homework. First, the rational course of action has to be demonstrably certain. As you correctly point out, hindsight bias is a real problem. Second, Luke has to show that the actor not only behaved irrationally, but specifically suffered from "motivated skepticism," rather than some other form of irrationality.
I'm looking for historical examples of "flinching away," so I can illustrate the concept to others and talk about motivated cognition and leaving a line of retreat and so on.
The ideal example would be one of motivated skepticism with grave consequences. Like, a military commander who shied away from believing certain reports because they implied something huge and scary was about to happen, and then the huge and scary thing happened and caused great damage. Something like that.
What examples can you think of?