Can you please post the output of

  gsettings get com.canonical.indicator.messages applications

It's likely that these webapps were added multiple times and have
different desktop files.

** Changed in: indicator-messages (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1233231

Title:
  Unity Web Apps appear twice in Messages indicator (Google News,
  LiveMail)

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