Do you have that problem if you copy the file to an another directory?
Could you attach an example of file triggering that problem to the bug?
What version of Ubuntu do you use? Are you sure that's not only the
directory which is reordered? Do you have the correct rights to read in
that directory? That's possible that nautilus mask the file on clicking
because it figures it's not authorized to read it or something like that

** Changed in: gnome-desktop (Ubuntu)
Sourcepackagename: gnome-desktop => nautilus
   Importance: Medium => Low
     Assignee: (unassigned) => Ubuntu Desktop Bugs

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clicking on a file makes it disappear (like it was deleted)
https://launchpad.net/bugs/79351

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