I've seen this repeatedly, with often very serious consequences (complete failure of update from f15->f16 for example).
Between packages installed via pip, and packages installed via yum, some packages seem to switch between
e.g., numpy-1.6.1-py2.7.egg-info
being installed as a file and the same name being installed as a directory. This can cause subsequent rpm update (via cpio) to abort.
I don't know what's causing this, but IMO this is a serious problem.