So I made some shape keys for the lips, added some eyebrows and went to work on them, only to notice that they're being affected by the lip shape keys. How do I fix this? Do I have to make the eyebrows before adding these shape keys to the face? Also why and how are they affecting the eyebrows?
Shape keys are for when the modeling is done. Don't start adding shape keys and then expect to be able to add verts, edges or faces later. You may still move verts around a little, but results are sometimes unpredictable.