I can tell you it's not a nif issue, I have seen it happen to vanilla creatures. there was a bug in Supreme Magicka when using Paralyze or Frost damage (Which had a chance to Paralyze when using SM) to affect the base of the creature. So if I got close to any creature type that had been Paralyzed before it would fall over stupid in the place it spawned. If it was killed on a slope or hill, each of it's limbs would stretch out and havok down the hill but it's body would remain in the place it died.
Probably a bug with havok in general, but if it's consistently happening on WarCry specific creatures than something must be preventing them from animating properly when they die.
Thanks for the answer. It only happens with armored skeletons from WarCry. I have a thread on TES Alliance as well as I didn't get any response here and a likely cause was given by Windmill Tilter:
The problem is caused by the way the skeleton flies apart on death, it drags portions of the armor with it causing the armor to stretch. The easiest solution is to alter the skeleton.nif so it doesn't fly apart on death. It's a bit tricky to do but there are a few of them kicking around.
No idea myself really. We'll see how it goes - perhaps it can be fixed that way.