When I open qBittorrent or calibre they show for a moment in the dock and then go away. I am using qBittorrent v3.3.1 which is in the official repository and calibre v2.70 which I downloaded from calibre website.
I searched around and found two questions relevant to my problem. This question is similar but the solution does not work for me. I already had the Show Unpinned option ticked.
This question deals with multiple icons of same application.
I found a workaround for qBittorrent. There is a qBittorrent icon at the top when it is running. Clicking on this icon brings up a menu with a option Hide. Clicking Hide twice in this menu brings back qBittorrent icon in plank.
The list of softwares seems to be growing. Now mousepad and virtualbox also do not show up in the dock.