On this other thread: trying to download OS X El Capitan but keeps saying busy try again
I found this link: macos - Force Re-Download of El Capitan from the App Store? - Ask Different
This part, and what follows, about moving the Installer may be relevant:
Check your main Applications folder or - if you have moved an older OS X El Capitan installer.app to a different folder - this second folder for the app. I have a "Installer" folder in my user folder dedicated to OS X Installer apps (the latest but also older OS X versions) and the single installer.apps will be downloaded (or "updated" to the latest version) there.
I had moved the original installer to Downloads so when I tried to install the new update App Store downloaded a new installer which installed the older version.
I moved the original installer back to Applications and now when I go to the El Capitan page (clicking on the El Capitan link in the update window) it now gives me the option to "open" rather than "install". Clicking on that opens the old installer rather than downloading a new one as it did before.
I've now taken the old installer out of Applications and into the Trash, without emptying the Trash, and the phantom update has now disappeared.
Out of interest I tried putting the installer back in Applications to see what happens. The "update" has reappeared!
It seems the fix is to put the original installer in the Trash.
But is that OK?
Should the installer be deleted after an install?