For instance, I've been the madman and had the scout's arrow nail me 3 seconds into my stalk. It did the damage and the slow like it normally does.
You may have been visible to the enemy at the time. Scout may have placed an eye/wards that you didn't notice. The only way to really test it is by getting the match id for a proper review. I've never seen it work improperly. If scout targets you with an arrow - and it launches -> you invis while it's mid-air - it'll probably hit you because it's incredibly fast moving, and the fade time wouldn't block it. If the arrow hadn't launched yet - then you were still visible to the unit because it does cancel if you go out of sight from scout.