This is a bug in GtkStatusIcon, not in Skype. Here is the patch for
gtk+3.0: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=910635#26

** Bug watch added: Debian Bug tracker #910635
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=910635

** Also affects: gtk+3.0 (Debian) via
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=910635
   Importance: Unknown
       Status: Unknown

** Also affects: gtk+3.0 (Ubuntu)
   Importance: Undecided
       Status: New

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https://bugs.launchpad.net/bugs/1773682

Title:
  Skype notification area icon corrupted

Status in Ubuntu MATE:
  Invalid
Status in gtk+3.0 package in Ubuntu:
  New
Status in gtk+3.0 package in Debian:
  Unknown

Bug description:
  System Version: Ubuntu MATE 18.04
  Package: mate-panel 1.20.1-3ubuntu1

  How to reproduce:
  - log in with new user profile
  - install Skype from Software Boutique
  - launch Skype

  => icon in nofitication area is corrupted (see screenshot)

  This is already noticeable on default panel size, enlarging the panel
  makes it even more obvious with lots of duplicate Skype icons
  appearing.

  This bug does not appear on the GTK2-based Ubuntu MATE 16.04 running
  the exact same Skype version.

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu-mate/+bug/1773682/+subscriptions

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