NBC contradicts the Times because the Times is claiming, or at least implying, that the HX vanished while the facility was under coalition control. The embedded reporter's testimony shows that it was either removed by the Ba'athists in advance of the invasion, or hastily removed during the invasion.
Either way, while it's distressing the bad guys presumably have access to the stuff, it's not a political hit against Bush or the US military that the stuff isn't where the IAEA said it was.