This may just be a shot in the dark, but it might be that you have doubles of some of your faces. If you extruded a vertex loop a couple of times without realizing it, you may have a few faces (or sections) that double up, but occupy the same space. So, with slight movements, like in a character's idle animation, it might be possible that the different sections of double faces are catching the light and showing up funny. It's just a guess though. You may want to go back into your modeling program, select all of the vertecies, and remove any doubles.
Edit: Afterwards, make sure that the normals are all facing out again, since if you have double faces, it's very likely that they have different normals.