The spark that rendered the Fremen so dangerous was the arrival of the Lisan Al'Gaib. The seed for that was planted by the Bene Gesserit, who aren't exactly known for being forthcoming with their secrets. And not even the Bene Gesserit seemed to fully appreciate Paul's potential until shit started hitting the 'thopter.

No mentat nor governor could have foreseen the disastrous consequences of a secret plan, upset by an unplanned deviation, escalating upon contact with a people largely hidden from galactic attention.

What the Emperor and Harkonnens did plan was the fall of House Atreides, and that went as smoothly as any plan could go: maneuver the Atreides into an awful position where the limited administrative capacities of a military aristocracy were stretched thin, plant a traitor that should have been incapable of treason, enabling the use of weaponry thought outdated, bolster their forces with elite troops, abduct the Atreides instead of actually killing them to create plausible deniability, make sure that the Bene Gesserit mother doesn't get to use her Voice. They stacked the odds in their favour meticulously.

But any plan is subject to unforeseen deviations, and that deviation was Paul's own command of the Voice, leading to his and his mother's escape from their captors, subsequent escape from the Sardaukar, subsequent survival of the storm and most fatally the awakening of Paul's abilities.

I don't think you can fault any commander for overlooking that the exclusively female Bene Gesserit witches might have trained a male in their art, who might then proceed to survive a storm, find shelter with the savages out there, be hailed their messiah and come lead those undisciplined desert dwellers in a successful assault on a well-kept military force.