This isn't just a problem with HA, it's an issue with all ranged. You get what looks like a perfect shot, but turns out it was a miss. Or on the other hand, it flies way off the target, BOOM headshot.
I don't know for sure, but if I had to guess, it might be an issue that lag causes the server and client to use a different seed, so the actual arrow is using a different seed than the one you see is.