This is all guesswork, but from what I've seen, when animations are played on actors the collision detection is a bit hit-and-miss. If you have an NPC sticking his arm out whilst standing next to a wall, the arm may well go through the wall. Presumably what is happening is that the animation is played and then Havok comes in to try and work out the consequences of the new object shape, but if collision surfaces have become too far merged or interlocked it is unable to separate them. I found this out the hard way when I navmeshed too close to a static object (a bar) and had an NPC get her arm stuck in it whilst walking past.
Couple this with the fact that the navmesh in the wasteland often dives underneath the scenery and it might explain why scorpions and the like often get stuck. I think the game tries to spawn actors on the navmesh, and if it's underground, Havok may not always be able to sort out the consequences. It also occurs to me that the shape of the actor might play a part. A tall, thin humanoid would spawn with only a small proportion of their body below ground, whilst a low, flat scorpion or ant might have the bulk of their body below the ground surface, and the proportions above and below might have an impact on how Havok determines what goes where.
In my experience the problem was more prevalent in NV than in Fallout 3, and from what I've seen the navmeshing in NV is a bit more... unpolished, than in Fallout 3.
Like I said, the above is only guesswork and might be total rot, of course.