A locked door must be opened - and sometimes things need to be stated explicitly. Yes I know that link made no sense.
wcfin8 (email@example.com) writes:
We don't hear or see any mention of the flood until AFTER Cortana and MC disable the security systems on the installation after being locked out while looking for the silent cartographer:
CORTANA: "we can't proceed unless we can disable this installation's security system"
Later we hear a marine say that the covenant worked hard to lock the door where Keyes and his squad were overwhelmed by the flood. So maybe the covenant were already in there when the flood was released, unbeknownst to them, and all they could do was lock the door and run. Backing this up is the fact that the humans find out that the covenant already has a name for these new enemies "the flood", which lends credence to the idea that the covenant already knew they were there. If they knew they were there and knew what the flood was capable of, I find it unlikely that they would release them.
In Assault on the Control Room, Cortana says something that most people, including myself, assumed meant that the covenant released the flood:
Cortana : Oh, those Covenant fools...they must've known, there must have been signs!
But maybe she didn't mean that they should have known they would release the flood (because she did that herself) maybe she means that the covenant should have known that Halo isn't the Forerunner weapon, The Flood are.
Also in AOTCR, Cortana says: The weapons cache he's looking for, it's not really-we can't let him get inside!
If you follow that sentence and finish it logically, the only solution is that the weapon isn't halo. Why else would she say the weapons cache he's looking for is "not really-". The Humans think the weapon is Halo so That is the only thing he can be incorrect about. So maybe the Flood was a forerunner weapon, a sort of biological warfare. And just like any biological weapon, it has to be stored and locked up with ridiculous amounts of security, until someone or some A.I. decides to override those securities. Also note the word cache, by definition that does not fit in a description of Halo.