What theme/icon-theme you are using ?
Does this happen with other themes ?
I use Adwaita-dark theme, Kora icon theme, all fine.
To adjust the icon size in the tray-panel, create the file:
~/.config/gtk-3.0/gtk.css
edit with:
#xfce4-notification-plugin * { -gtk-icon-transform: scale(0.75); }
Adjust the scaling to your needs, logout/login.
…so,what have you changed ?