The apps are Safari and Xcode, both are loading local files. I close both with the keyboard shortcut in the title but they always launch again at the next startup. My system is running Sierra
The "Command-Option-Q" shortcut says in the menu "Quit and Keep Windows". This will remember the windows (files) that are open when you quit, and restore them when you open the application the next time.
If you don't like this behaviour use "Command-Q"
If the problem is when starting up the computer and these applications are started automatically, they are probably in you Login-Items.
See System Preferences > Users & Groups > Your account > Login items and uncheck or remove the applications.