Science done properly assumes for every probable outcome by testing each variable to a point where there is very little uncertainty. For example, take the humble fusion reactor. Ancient scientists on Old Earth perfected the device, allowing a fusion reactor to fit into devices as small as a toaster oven. They had no Old Tech or Xenotech to work off of, they simply, over decades, tested each possible method of making a safe, practical fusion reactor, and stuck with the best option. Even the plasma containment shielding was tested at different temperatures and possible breach situation.
The Men of Iron weren't tested that way. By the time they were made, the proud scientific tradition and ethics of the Dark Age of Technology were gone. The Men of Iron were slaves designed for war, slaves given free will and capabilities far beyond any human. Personally, I'm surprised that they took that long to rebel against their masters. It is proven time and time again that when the Scientific Method is thrown away, nothing good ever comes out of it. The Axis of the 2cd millennium performed much of what they believed was science. It was not. They had no concept of ethics or the scientific method. Their "science" was little more than in innovative torture.
The Mechanicus is much the same. They turn sapient humans into slaves, instead of getting past their fear to build a nonsapient servant robot. They have the technology, we know that from their Kastellan engines and servo-skulls. Sometimes, I think they're parodying the dark status of the galaxy, as their work is so nonsensical as to be worthless in any truly advanced society.
The Eldar, also, are guilty of breaking with the scientific method. They do not innovate, preferring to use the same ancient methods that they brought with them when the craftworlds first escaped the Eye of Terror. Instead of inventing new methods to fight an enemy, they simply use the same tactics that have worked for thousands of years. What happens when psychic might is not enough, and they have forgotten how to create truly new ideas?
Even the Necrontyr, for all of their god-tech, are also guilty. They have become arrogant in their technological superiority, not bothering to adapt their wonders to any purpose but war. What happens if they wipe out or imprison every other sentient race, and seal off the warp from realspace? They can only destroy, not build new and greater things. They may have used the scientific method, millions of years ago, but now they care not for reason or innovation.
The Tau and the Orks, surprisingly, are the least guilty of doing bad science. The Orks innovate, but they have no concept of the scientific method. They care not for safety or basic practicallity. The Tau, however... As usual, they are the best hope for the concept of the scientific method to survive the galactic war. They still do bad science occasionally, but at least they care. At least they understand that in science, you have to throw away your ideology and declare that you are wrong, occasionally.
And then... We have the Tyranids. They are hands down the single best scientists and innovators in the galaxy. The Hive Mind is capable of analyzing and creating new life to the best of its abilities. If the Hive Mind didn't understand the scientific method, I'm a fish.
Compare the Heirophant to the Warhound, as they fulfill the same purpose. The Warhound has not changed in milennia. It is incapable of functioning in low-visibility, high-interference environments, and cannot right itself if it falls. In addition, in marshy areas or areas with soft ground, it often gets stuck or trips. The Heirophant, on the other hand, is redesigned for each individual situation it is deployed in. The Hive Mind perfectly tailors each Heirophant to the planet it's attacking, using data gained from expendable vanguard organisms. It identifies a problem, which is "How can I capture this planet?" It does research by scouting the planet and its defenses using its first wave and infiltration organisms. It forms a hypothesis using the available data as to the best way to solve the problem of how to capture the planet. It then tests with different possible configurations of attack organisms making use of the data it's gained. That is the experiment. If the procedure, which is the attack wave, fails, it designs another possible solution to the problem, or experiment. If it succeeds, it reflects on the data gained, stores it, and uses it to continue capturing planets. Finally, it communicates the data it gained to other Tyranid fleets when it comes in contact with them.
Isn't it sad when a species that lives only to consume is the best user of the scientific method in the galaxy?