Yeah, I can see how that's confusing; I need to clear up the phrasing. The rep loss is for defeating the expedition as a whole, not the fleet. For example, if you fought the expedition's fleets separately, you'd only lose reputation once, on defeating the whole expedition. Or, if you let your system defenses handle them and avoid fighting them yourself, you'd still lose reputation when the expedition as a whole is defeated.
Basically, defeating the expedition will always reduce your rep, but it's not on a per-fleet basis.
Edit: there, cleaned it up - the intel now says that defeating the expedition will cause a small reputation drop.