The test itself wasn't fatally flawed, it snowballed when they had an unrelated engine malfunction.
Several minutes into cruise, the right engine inlet’s automatic control system malfunctioned, requiring a switch to manual control... Without proper scheduling, disturbances inside the inlet could result in the shock wave being expelled forward–a phenomenon known as an “inlet unstart.” That causes an instantaneous loss of engine thrust -- TFA
It wasn't unknowable or even an unexpected situation, those engine unstarts were common until they worked out the control system dynamics. They were moving fast and killing test pilots right at the beginning of being able to use computers to simulate flight. Exhaustive simulation of all circumstances might not have been possible with the available computer time, or honestly it is quite possible nobody thought to do it.
Test pilots though are generally aware of and on board with the risks. Unfortunately simulation isn't all it's cracked up to be and very often aerodynamic models are trustworthy only after they have been validated experimentally for the specific scenarios they apply to even now. Nevermind half a century ago.
Right, the engine unstarts were a common and expected problem, but the key is that I don't think they were in any way predictable, other than being limited to certain condition regimes that included basically everything except subsonic flight.
That would be a lot of unknown conditions to test for.
Several minutes into cruise, the right engine inlet’s automatic control system malfunctioned, requiring a switch to manual control... Without proper scheduling, disturbances inside the inlet could result in the shock wave being expelled forward–a phenomenon known as an “inlet unstart.” That causes an instantaneous loss of engine thrust -- TFA