This seems to be a kde specific and LibreOffice specific problem because this hadn't occured in gnome.

Steps to reproduce:
Open file with LibreOffice on one virtual desktop.
Move to a different virtual desktop.
Open file with LibreOffice on the virtual desktop you moved to.

Here is a demonstration video:
https://www.youtube.com/watch?v=uFOUtcaAW8k

Same issue.

More than that, when I have multiple Calc documents opened in different virtual desktops, opening a new document moves all Calc windows from all virtual desktops into one virtual desktop. That's a bit excessive.