Recently one of apps is not showing in the Application Switcher, the Dock or even in the menu bar. The only way that I have found to get to it is via Mission Control or Launch Pad. And even when I do this it still does not show up in the menu bar so I can't access the menu items (preferences etc.) The application in question is Fantastical 2 (an alternative Calendar app).
User error ... I had to use the command+comma shortcut to change preferences. I had foolishly checked "Hide icon in Dock" not realizing that it would also hide it in the application switcher.