I have the exact same issue. Win10 - 1909 ; Stardock fences 3.0.9.11
Here's what I've found. The shortcut is usually on the wrong screen, at the right Y position but shifted to the left (towards negative X)
If I make multiple shortcuts without clicking on the desktop in the process, they eventually get on the correct screen and at the right place. But if I click on the desktop, then make another, it restarts this strange behaviour
I'm available in case you need more informations or testing
Left is the primary monitor (primary desktop), where the icons should go. Right one is the 2nd, the icon overlap but is at the correct Y level (height), so the 3rd icon
End of Kartzul's quote
Hello,
Sorry to hear you are having issues. This is known issue and I believe it has been logged internally. For temporary solution. Please set desktop icons sorting to none

or send all new icons into temporary Fences by using Fences auto rules. Follow below steps :
1) Create a new Fence. Give it a name.
2) Set that new fence rule so that all new files go to that Fence.
From now on all the new icons/files/program move to your desktop Area will be automatically move to that New fence.
Basj,
Stardock Community Assistant.