xml-commons-apis from Core removes xml-commons-apis12 from Extras, because the latter contains "Provides: xml-commons-apis = 1.2". As such, xml-commons-apis upgrades xml-commons-apis12 and removes it. If you want both packages to coexist, remove the Provides. For RPM background refer to the current gtkhtml38 thread on fedora-test-list and the ticket linked therein.
hmm, I really should have known better than that (since I did open a bug about the same type of situation: https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=233713). This has now been built into rawhide.