I think with yum you can use the --exclude=package
switch to tell it the packages you do not wish to update (the conflicting ones). I'm not 100% sure but I think you need one --exclude= per one package, so two packages needs two of these switches etc.
Example (from the top of my head):
yum --exclude=dbus update
If you are sure the packages are installed, as rpm packages, but it seems not all programs "see" them, try
which should rebuild your rpm database. It's usually not needed but I've had it help me once.
Apt won't do probably much more, it's just a package manager as is yum too. The bad side of package managers is that sometimes you may get them go crazy, and results are something like this situation now seems to be; however, if the programs you said yum can't "see" are installed were installed by other means than rpm packages, try to remove them and install from rpm packages or trough yum. Also upgrading from a previous version of Fedora instead of doing a clean install may cause this kind of trouble (I believe this is one of the main reasons why people are discouraged of updating this way, and encouraged doing a clean install).
Try the --exclude=package
option if it helps. You could try forcing a package install too, but I wouldn't go ahead with that if it's about dbus.