Program doesn't remove files to Trash

I use FFS to make mirror backup to my another internal drive.
The problem is that the app doesn't move all files on "right" side to trash. It gives a message everything went fine but eventually a lot of files aren't removed - sometimes it removes only a small part, sometimes it doesn't remove anything, but almost never everything. I guess it depends on number of files to delete.
The function works fine when deleting files permanently (without using Trash).

Binary non-flatpaked version from official webpage works fine so I guess it's a flatpak issue.