There wasn't much substance to the New York Times's report, and as an outsider, Facebook's official reply--corroborated by Tim Cook's statement about Apple's actual use of the reported APIs--seems perfectly reasonable to me.
But dogpiling on Facebook is popular right now, whether it's deserved (Cambridge Analytica) or not (this), so the actual facts of the matter will be secondary when politicians evaluate whether to hop on the bandwagon.