The issues could be a blessing in desguise since it's showing files that are using resources that you no longer use.
Try running the combo updater to refresh your files. This has helped other users with this last update.
OS X Mavericks 10.9.3 (Update (Combo)
http://support.apple.com/kb/DL1746
MORE INFO ON WHY RUNNING COMBO FIXES ISSUES
Apple updates available from the Software Update application are incremental updates. Delta updates are also incremental updates and are available from Apple Downloads (software updates are generally smaller than delta updates). The Combo updates contain all incremental updates and will update files that could have become corrupted.
Combo updaters will install on the same version as they're applying--no need to roll back or do a clean install. So if you think you've got a borked 10.8.4 install from a regular update, just run the 10.8.4 Combo Updater on that system.
"Delta" updaters can only take you from one version to the next. For example: 10.9.1 to 10.9.2. If somehow the 10.9.2 is missing something it should have, and that something isn't changed between 10.9.1 and 10.9.2 it will still be stale after the delta update.