This is a very common question. Skinning has NEVER worked correctly, it's not a bug. nothing to see in the log, the devs have to fire up a skinning toon themselves or at least a video.
No matter how you set (or dont set) the Ninja skin and Pull more settings, whether or not you are AOEing mobs, the bot will skin TWO MAXIMUM and only two mobs. It will loot EVERYTHING, but skin only (up to) two. after it skins two, it will run off searching for next target, leaving the unskinned bodies behind forever. THIS HAS NOTHING TO DO WITH "STILL BEING IN COMBAT". it's not in combat, it simply resumes trying to find and kill fresh mobs even if surrounded by 10 skinnable bodies. ALWAYS BEEN LIKE THIS, NEVER FIXED. Source: 100s of hours skinning in Nagrand and in previous expansions.
The only real downside is that you're getting less skins per hour. Skinning still works fine.