"They seem most persistent in their attempts to access restricted areas."
It sounds to me like they weren't allowed to release the Flood, but forced their way in (e.g. explosives).

"This mining facility predates Installation Alpha by several hundred years. It was retrofitted to research possible offensive and defensive measures against the Flood. Indeed, I designed and oversaw the construction of this facility's various outbreak management systems."
Also, the facility wasn't intended to hold Flood in the first place. It was retrofitted.