This seems to be an issue with the KOTOR 2 animation. As I recall, the robes have a custom idle animation to reduce clipping with the arms and the cloak. But the animation appears to have a glitch in it. I'll see if it's possible to improve that idle animation for both games when I get a chance.
These are issues with Bastila and Jolee's original body models. Their skirt flaps are dangly meshes—they aren't animated. They move based on the wind and some other physics. Very limited physics.
I looked into weighting Bastila's skirt flaps to the robe bones, but I couldn't get it quite right at the time. I didn't attempt it for Jolee. I was able to do it for Juhani, because she only has the back flap and that lined up with the cloak fairly well. Maybe I'll try again for the other two, but it didn't seem very promising the first time around.