I also experience this nasty bug. It is present for many years now. Up to 
Ubuntu 16.04 I used the script from comment #37
https://bugs.launchpad.net/inkscape/+bug/418242/comments/37
but now it stopped working. Hence I updated this shell script following the 
remarks in comment #74
https://bugs.launchpad.net/inkscape/+bug/418242/comments/74
It is workaround, but for me it works perfectly. My Inkscape version is 
0.91r13725 on Ubuntu 16.04. I hope it will help some of you.
In general it is much better to manually edit the files which generate these 
nasty errors as is explained in comment #74, but in my case I need to do this 
on more then 10 different desktops, hence the script is much more useful.

** Attachment added: "InkscapeFix_09.2016.sh"
   
https://bugs.launchpad.net/inkscape/+bug/418242/+attachment/4743477/+files/InkscapeFix_09.2016.sh

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https://bugs.launchpad.net/bugs/418242

Title:
  Incorrect call to output plugins (with persistent error message) on
  copy

Status in Inkscape:
  Triaged
Status in inkscape package in Ubuntu:
  Triaged
Status in inkscape package in Arch Linux:
  New
Status in inkscape package in Debian:
  Confirmed
Status in Gentoo Linux:
  Unknown

Bug description:
  UPDATE: After further investigation it turned out to be a problem related to 
the copy operation, in combination with a totally unrelated running Java 
program (FreeRapid).
  Reading some followups and other bug reports, it seems to be caused by the 
new clipboard management system (introduced as a fix for the bug #170185), as 
reported in bug #421597

  So far these applications are known to randomly trigger an input/output 
extension (on linux):
  - FreeRapid Downloader
  - jDownloader
  - xfce4-clipman-plugin 1.1.3
  - Netbeans
  - xfce4-settings-helper (Xfce 4.8)
  - Team Viewer (teamviewerd 10.0.36)

  -----

  The original report was this:
  I'm getting this error when I try to edit a text object created previously 
with a font that's not available in this system.
  It looks like Inkscape has problems to resolve the font substitution and 
displays the error message in a popup window that keeps appearing again and 
again, leaving no other remedy than closing inkscape and reopening it.

  The error message is attached.

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