I was not expecting this! | Halo 2: Anniversary 

It was actually explained in Combat Evolved (although very briefly and poorly); the Flood are incredibly adaptive. Once they take over a host, they gain all of its knowledge; force deployments, weapons and craft usage, etc. In the first game, Guilty Spark was worried about the Flood repairing a Covenant ship to escape the ring. It's likely a Flood combat form took a ship back to High Charity with some carriers or just Infection Forms and thanks to all the commotion and excitement, went unnoticed.