Apps in El Capitan won't close when clicking the red close button Apps won't close when clicking the red close button in El Capitan. The "open indicator" stays on the app icon, the icon stays in the dock even if "keep in dock" isn't checked, and the app shows up in alt-tab. This is very odd to me since in Yosemite they closed just fine. I don't mind so much if the app stay open in the background, but if I use every app in a day and close them all, they all still look like they're open. This is confusing, and to me makes the close button no different than minimize. In fact, if you enable "minimize windows into application icon," the close and minimize basically act the same. Is this a bug, or a change? Any idea how to fix it? I saw a post recommending to uncheck "Restore windows when quitting and re-opening apps," but this option seems to be gone.

Edit: I realized that when I was using Yosemite I had cDock installed. Maybe this program let me limit app indicators to apps with open instances in an old version. It doesn't appear to now.
There is a difference between closing a window and quitting an app. Many apps continue running even if they have no windows open, although newer versions OS X can close them if it needs the RAM (if the app is coded in the appropriate way). 

If you want to be sure the app is removed from the Dock and ⌘ Command Tab switcher, use ⌘ Command Q or App Menu > Quit.