Certainly this is not the normal behavior, but I think I may have an explanation. If you have multiple users on your Mac, it sounds as though whichever user received the update may not have administrative permissions on the computer. To check, go into System Preferences, click on "Users & Groups," depending upon your individual setup, you may need to unlock the panel by clicking the padlock on the lower left, hilight the user who attempted to install the update, and look at the checkbox labeled "Allow user to administer this compter." If that box isn't checked, that user won't have permissions (by default) to install anything into the /Applications folder, so anything they install will go into the ~/Applications folder instead.
It's hard to say if this will fix your issue in particular, but it's worth checking.
