They should have. I know the 787 has electronic checklists, but I have no idea if the aircrew can override warnings like that, or how present such warnings even are in the cockpit. I'm assuming one pilot is reading off the checklist, and the other is executing/declaring green, but maybe a faulty indicator, or crew misattention? Or something else?
Obvs it will have to await box recoveries and a full investigation, but I struggle to understand how in such an automated airplane how the crew might be unaware that the flaps weren't down. Of course, I'm not a pilot, so caveats about back-seat driving etc apply.