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.
UPDATE:
The list of softwares seems to be growing. Now mousepad and virtualbox also do not show up in the dock.