El Capitan update 10.11.1 stuck at installing update in app store
You mean you are still in App Store; you haven't actually launched the Install OS X El Capitan file yet [or it hasn't auto-launched]? 

If the installer isn't yet running, you're safe to cancel it. 

My App Store download errored at the last second &amp; when I clicked the Update button again it suddenly realised everything was in fact fine.
Check if you have the installer app in your Applications folder. If you do, then it actually downloaded OK &amp; you ought to be able to double-click it to continue.

As always on a major update, make sure your backup is up to date; &amp; as a double safety-net, remove or disconnect your Time Machine drive until you are happy all went well with the update.