It shows the favorite applications, and properly shows the orange dotd on the left of the running ones, but not the running ones if they are not favorites.
From dconf-editor, org->gnome->shell->extensions->dash-to-dock->show-running is set to on. In the picture it is possible to see the options in dconf and the behavior of the dock:
neither the terminal nor dconf-editor are visible in the dock. The applications are normally visible elsewhere (for example clicking on Activities).
33 Answers
I also use Dash to Dock gnome extension, so I was able to fix this by disabling Use built-in theme in the Apperance section:
After doing this, the indicators were now showing up
I had "Use builtin theme" disabled already as per the above answer, but running applications still were not showing.
I enabled and disabled "Use builtin theme", and now the running applications are showing. Even when I re-enable "Use builtin theme" the Running Applications are showing.
Perhaps the bug is that you have to change something in the config for it to work.
Created bug in dash-to-dock:
In my case, I have multiple monitors attached to my laptop and every time I was clicking on nautilus it was opening up a new window and was not showing the little orange running dot that Ubuntu shows for running instance of the program.
I managed to solve this by turning off "isolate-monitors" flag in dconf-editor, /org/gnome/shell/extensions/dash-to-dock/isolate-monitors
