The thing is that those are not small statistical disagreements.
The maximum tsunami+tide they designed for was 5m. Design parameters said that you should have a wall 2x what you think you need so they built a 10m (about 30 foot) wall.
Two independent teams came up with realistic tsunamis near that 10m wall (one over and one under), so they should have changed their wall requirement up substantially. But they argued themselves into believing that 6m was a realistic maximum then did nothing.
Their estimates were also out of line with actual tsunamis experienced elsewhere. Tsunamis in recent decades from earthquakes similar to the ones that they knew could hit the area have ranged from 3-30m. Even a 7.0 earthquake managed to create a 12m tsunami in New Guinea.
The actual tsunami was 13m.
The most telling point is how the response afterwards has shown lessons not learned. For example The United States National Research Council of the National Academies had a 21 person panel conduct 18 months of interviews with a wide variety of technical experts on how the disaster could be prevented here. NOT ONE of the members of the panel or the people interviewed was an expert on tsunamis. The author's of the paper clearly believe that if you're studying the aftermath of a tsunami, you should at least talk to someone who studies tsunamis...
If the paper is correct, it is a question of time until somewhere in the world we have another entirely preventable major disaster because local officials underestimate tsunami threats that current knowledge is more than sufficient to predict. Of course enough things can go wrong that the next big disaster won't be that. But that preventable disaster is coming...