I can absolutely understand your doubts as I would probably say the same if I had never encountered this (and it really doesn't make any sense as I do believe the responsible devs are kind of skilled at what they do).
All I can tell you is that it happened for me and it did happen often enough to be noticeable and drive me nuts.
Regarding your 2. point (Skils and Hit rolls): I have no idea how exactly their hit-change is calculated. While you're right about not needing to roll for the skill itself, the skills do have a have a chance to hit / miss the target. So far I was under the impression that this hit-chance was the same as the shown chance when hovering over a target with the mouse, but maybe I'm gravely mistaken here and skills have a different hit-chance calculation than auto attacks. That actually would explain a lot.
Anyway, in my next playthrough I'll try to catch it on Video.
