I've had this issue multiple times yet. For me it has always been like
that: The content of a file gets overriden and therefore the system
fails to do something.

Last time my system settings broke completely. When doing a "cat 
~/.config/dconf/user" I got:
"/opt/click.ubuntu.com/com.ubuntu.developer.webapps.webapp-gmail/1.0.25"
And after a reboot it now shows this:
"/opt/click.ubuntu.com/com.ubuntu.developer.filip-dobrocky.2048native/0.2"

Deleting "~/.config/dconf/user" did the trick for me.

Some other time system updates didn't work and doing a "cat 
/cache/recovery/image-master.tar.xz.asc" revealed it contained the following 
content:
"/opt/click.ubuntu.com/com.ubuntu.developer.majster-pl.utorch/1.6"

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https://bugs.launchpad.net/bugs/1387214

Title:
  [TOPBLOCKER] file corruption on touch images in rw portions of the
  filesystem

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