Skype 8.20.0.9 and Ubuntu are working fine. No issues. This is more of an aesthetic thingy. Anyways, has anyone face with a double skype icon in the Systray?

If you have, how can this be fixed?
As a workaround, change EXEC in /usr/share/applications/skypeforlinux.desktop from
Exec=/usr/bin/skypeforlinux %U
to
Exec=env XDG_CURRENT_DESKTOP=Unity /usr/bin/skypeforlinux %U
You have to make the same change to ~/.config/autostart/skypeforlinux.desktop so that skype can stay in tray everytime system reboot. However, it seems that skype will undo the change of this autostart file everytime it restarts. My solution is to make this file read-only, like
chmod 440 ~/.config/autostart/skypeforlinux.desktop
As mentioned here: System tray icon in xfce - Microsoft Community, - there was same issue on Fedora 28 with GNOME desktop. It should work for Ubuntu as well..
The electron framework appears to have issues with upscaling the tray image, but does not seem to have a problem with downscaling the image. So an alternative work-around for the current situation is to replace the small (16px) images with larger versions - and I suspect that even without this issue, in most cases, downscaling a 256px icon to (arbitrary) target tray size will look nicer than upscaling the extra small icons.
Until this is fixed in electron or worked around in skype by using larger icons by default, you can work around it yourself. To do so, one needs to unpack
/usr/share/skypeforlinux/resources/app.asar(using electron asar tool), replace the images in<unpacked-dir>/app/images/tray/linux/, and pack it back. The tray icons are already provided in two versions, 16px and 32px (HiDPI, @2x name suffix). So if your tray size does not exceed 32px, you can simply copy the 32px versions over 16px ones.
sudo apt-get install npm
sudo npm install -g asar
app.asar
asar extract /usr/share/skypeforlinux/resources/app.asar ./skypeapp
app.asar and replace old one
asar pack ./skypeapp ./app.asar
sudo cp ./app.asar /usr/share/skypeforlinux/resources/app.asar