Has it ever been pointed out as to when the Covenant first encountered the Flood? I did not think Halo:CE was the first time for them, but I may be wrong. Does anyone know?

The outbreak on Alpha Halo was the first time either humanity or the Covenant encountered the Flood, up until they were revealed to be in Halo Wars. So now things are a bit unclear, but we can assume that the Flood in Halo Wars is first contact for both humanity and the Covenant.

Previously it was maintained that Alpha Halo was the first time the Flood had been encountered, but it seems the story is being retconned a bit by their inclusion in Halo Wars.

well at the end of assault on the control room in halo 1 cortana simply says it's "something horrible" that the covenant excavated so i'm pretty sure that the level after was the first encounter

*sigh*

Halo lore is definitely my favorite lore.

Could you imagine a situation where the Halo Wars characters did indeed meet the flood but such information was known to either the UNSC or the Covenant? That might explain the paradox while still keeping the lore pretty solid.