I understood the issue to be that the Fringe team failed to think fourth-dimensionally. They disrupted that particular shipment, possibly causing havok and large-scale damage in the future doing so. However, these shipments are being sent through time. If we assume that in the future, their interruption of the shipment succeeded, this would have caused major destruction in the future. But then the Invaders would have just rebuilt that destroyed infrastructure, maybe even taking years to do so.
So once they've rebuilt their future shipping system, what would their first step be? Resume the last shipment, sending the rest of the shipment to the same destination time and place. In the 'present', the Fringe team saw this as a nearly uninterrupted shipment as a result.