Is this an El Capitan bug? I've noticed in more than one app, when I go to File --> Open, the app opens the file in a new window instead of in the existing window. For example, in TextEdit, if you open a new document, and then from that blank document open a saved document, TextEdit opens the saved document in a new window and leaves the original document open as a blank document. This happens in other apps too. I never saw this happen prior to El Capitan so I'm wondering if it's a bug or intentional for some unknown reason.
TextEdit has always operated this way. Most applications do.