I do not completely understand how phantom hits work, but I have viewed some phantom hits in frame by frame, and I think I might know why it happens. It seems like the hit box doesn't actually connect at all. It's not just the 'border' of the hitbox hitting them, because there is no border. Each hitbox is just an area of an attack that does a specific amount of damage (changes over time usually) with a specific knockback (again, usually changes over time). If you view the hitboxes in frame by frame, you'll notice that the hitboxes stretch as they move. The stretch leaves behind what I call a 'hitbox shadow'. The hitbox shadow is, to my knowledge, a replica of the original hitbox. However, the hitbox shadow is usually not the part of the attack that hits, since a single hitbox shadow usually exists for only one frame. I am not always sure whether a given hit connects using the normal hitbox or its shadow, but I usually assume that it is the original hitbox. Usually when I view a phantom hit, it occurs one or two frames after the shadow. This really confuses me, because I don't completely understand how the hitbox stretching works, but I'm fairly certain that it is somehow related to phantom hits.
That's just my observations and whatnot, so if it doesn't make sense, oh well. Maybe someone else can explain it. -_-