: We know that the Flood were released by the Covenant in Halo 1 by mistake.
: However, if we assume that "the rings work the same way" then
: the Flood should be contained and neither side would intentionally release
: the Flood knowing now what they were capable of.

: Except the Flood weren't contained on Delta Halo.

: They were already out and around. So the marines in Sacred Icon wouldn't be
: expecting the Flood, even if they were briefed on the entirety of what
: happened on Alpha Halo. It was also very foggy and hard to see, it's very
: possible the marines saw what looked like Elites running around, called
: Keyes, then called back when they realized their mistake and cried out
: "Not Covenant!" in panic.

: It never really seemed out of place to me. I just assumed they weren't 100%
: sure that what they were shooting at was the Flood and that's why they
: worded it like that.

More to the point, Bungie's a sucker for the "we're screwed man!" moments in their Halo campaigns (like the intro of the Flood in "Floodgate".) It's more an emotional moment than a story beat, but I think it works on that level.

And off-topic, but I do agree that Quarantine Zone and Sacred Icon are probably my least favorite Halo levels.