Description of problem: It appears that both the emacs-el and emacs-common packages own the directory "/usr/share/emacs/site-lisp" and that seems wrong. Shouldn't all dirs be owned by exactly one package? See: rpm -ql emacs-el emacs-common | grep site-lisp | grep -v site-lisp/
No, both emacs-el and emacs-common include files in that directory and there is no problem with more than one package owning the directory. It ensures that the directory will be removed if all the packages with files in the directory are removed.