At the time, workers at Khrunichev were cutting pipelines and removing other components of the module's propulsion system, in order to reconfigure it from its original role as a backup to the Zarya FGB module into the MLM. For example, a set of six tanks, which would be used for refueling of the ISS during the FGB mission, were removed from the exterior of the spacecraft in order to make room for scientific instruments and for the attachment of the European Robotic Arm, ERA.
The official conclusion of the probe said that the contamination had stemmed from the "lack of methodological and technological support for the operations of cutting pipeline connections in the pneumatic and hydraulic system, PGS, which was needed to guarantee the meeting of requirements for ensuring the sterility of the internal cavities in the pipelines and system hardware." It is essentially bureaucratic speak for letting metallic dust formed during sawing off the lines pour into the interior of the remaining components.
According to one legend circulating at GKNPTs Khrunichev, the workers who were sawing off pipelines from the module thought they were dismantling the entire spacecraft for scrap. That story would sound completely unbelievable if not for other almost as incredible incidents of carelessness, poor quality control and incompetence within the industry in recent years, such as the installing navigation sensors on a Proton rocket in the upside down position or loading a Block DM-03 space tug on another Proton with too much propellant.
It is most revealing of the overall systemic problems within Russia's aerospace industry.