Wow I can confirm this is indeed a bug.
I have a 49 warrior twink with axe skill 204/245 and I made sure to check before hand if I needed to max it out before doing BGs and all the posts about vanilla weapon skills in PVP told me I don't.
However I started noticing more and more attacks missing. At that point I basically assumed it wasn't working correctly on Elysium.
Thanks for posting this. I'll post on the bug tracker as well.