Perhaps the issue can be solved, and someone may bring a solution to the issue, but to my knowledge, I fear that may not be the case.
Gnome Shell moved away from icons on the desktop. Since Gnome Shell 3.28, icons on the desktop are not anymore supported. What you see, is one of the reasons. The technology to draw icons on the desktop is quite old, and does not play well with multiple monitors, high resolution etc. Developers decided the code would hamper further development of Files (aka nautilus, which provided the icons on the desktop) and dropped the support from 3.28 onward. Desktop icon support may return in the future to Gnome Shell, but will then be provided by a Gnome Shell extension,
Ubuntu 18.04 does supports desktop icons. They support this to the extent that the current Ubuntu version, 18.04, which uses Gnome Shell 3.28, ships with an older version of Files that still features support for drawing desktop icons.
There is probably not a lot you can do. Switching to nemo or caja will, besides from being quite complex, likely not solve your issue. Both file managers are forks of nautilus, and thus basically contain the same code to handle icons on the desktop.
An options to work around the issues is to change your working habits, i.e. turn desktop icons off and learn to use the dock to launch frequently used programs, and "search" in Files or the Activities overview to quickly get to your documents.
Alternatively, if you do not want to let go of your workflow based on having icons on your desktop, another desktop environment such as KDE or perhaps xfce (I doubt for the latter) may handle your configuration better . Budgie is yet another desktop, but it is strongly based on Gnome components and thus may also be problematic.