Incomplete Restore from Time Machine
My 2009 iMac running 10.9.3 was having problems with crashing apps and just plain acting weird. I decided to do a clean reinstall of Mavericks using my Time Machine backup. I discovered that the Time Machine Restore erases the disk during the process and that would give me the "clean" reinstall.
After completing the restore, Mail, Calendar, Contacts, App Store, iTunes, Maps, QuickTime Player, and iPhoto did not have their proper icons in the dock nor would they run. Also, all the Utilities including Disk Utility and Activity Monitor showed bad icons and would not run. Trying to open Disk Utility gives a message "You can't open the application "Disk Utility.app" because it may be damaged or incomplete." Safari, Notes, Preview and other non OSX system apps seem to be largely OK.
In desperation I downloaded the OSXUpdCombo10.9.3.dmg and reinstalled Mavericks. No change in the icons, but this time Mail did open but then crashed. I tried moving Disk Utility from my laptop to my iMac with dropbox but OSX will not allow me to replace the bad Disk Utility. Anybody have a clue as what I should try next?