The dot icon on the dock stays despite I have closed the app As the title clearly describes, the dot icon stays on dock for some apps such as VS Code, Terminal, Safari, and Finder despite I have closed the app. I am using Catalina 10.15.1. I have to manually right click those apps and select Quit in order to remove the dots on the dock.
The presence of a dot below an app icon in Dock indicates that the app is still running.

Clicking on the red  traffic light button in the app window title bar, doesn't quit every macOS app. The default behavior of a macOS is to not quit upon clicking the button.

Some apps are programmed to quit upon clicking the red  traffic light button, but most keep running unless you explicitly quit them by running the App Name → Quit App Name command in the menu bar, or using the keyboard shortcut Command + Q, or right clicking on the app icon in the Dock and selecting Quit.