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They do "wonder why" but then they list the various explanations and tradeoffs that have been made given the nature of the storm and the risks of the evacuation itself. The questioning is a rhetorical and slightly click-baity device, not actual disagreement, as far as I could tell.

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NPR followed up with Lieutenant General Honore of hurricane Katrina and Rita experience[1] and he disagreed with the mayor's orders.

[1]http://www.npr.org/2017/08/29/546978194/with-much-of-houston...

That is good information and a good point of view to have, but it doesn't change your earlier misstatement about NPR, itself, "wondering why", which is the thing I was trying to add context to. (maybe you didn't mean it that way, I'm cranky ;))

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