Comment 39 for bug 1277589

There is a strong suspicion as to the root cause being related to the update check causing two simultaneous processes doing the update. Two changes are planed: 1) to limit this to a single instance of system-update and 2) to download files first to /tmp then atomically rename

In the meantime users should change the Auto Download option in the Updates page in System Settings.
Change from Download future updates automatically from "When on wifi" or "On any data connection" to "Never"