“External incident responders were unable to provide the assurance EDA’s CIO sought, because doing so involved proving that an infection could not exist rather than that one did not exist,” the report said.
In the end, only six infected components were identified and according to the report, all easily fixable. But instead of taking that route, the EDA decided to physically destroy its hardware system.
They HAL 9000'ed themselves
Probably just a faulty logic center.
The novel explains that HAL is unable to resolve a conflict between his general mission to relay information accurately and orders specific to the mission requiring that he withhold from Bowman and Poole the true purpose of the mission. With the crew dead, he reasons, he would not need to be lying to them. He fabricates the failure of the AE-35 unit so that their deaths would appear accidental.
This contradiction created a "Hofstadter-Moebius loop", reducing HAL to paranoia. Therefore, HAL made the decision to kill the crew, thereby allowing him to obey both his hardwired instructions to report data truthfully and in full, and his orders to keep the monolith a secret. In essence: if the crew were dead, he would no longer have to keep the information secret.