As mentioned here: System tray icon in xfce - Microsoft Community - there was same issue on Fedora 28 with GNOME desktop.
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.
Solution by steps:
- Install required soft
$ sudo yum install npm
$ sudo npm install -g asar
$ asar extract /usr/share/skypeforlinux/resources/app.asar ./skypeapp
- Replace smaller icons with bigger ones
app.asar and replace old one
$ asar pack ./skypeapp ./app.asar
$ sudo cp ./app.asar /usr/share/skypeforlinux/resources/app.asar
With slight modifications works for Debian 9 as well.