Thufir had a strong reputation as a cunning and one of the best mentats in the universe, but in the first half of the novel it might be hard to see, as he was tested and failed. His biggest blunder was to seriously underestimate the number of Sardaukar the Emperor would send to attack; he estimated no more than 2 brigades, but in reality there were 50 brigades (or 5 legions).
Why did Thufir make such a gross miscalculation? We know that the Emperor wanted to completely annihilate House Atreides, hence the huge number of forces sent, which raises the question: what did Thufir think the Emperor wanted to do with 2 brigades?