Fixed the problem.

Removed the plugin org.gnome.shell.extensions.dash-to-dock isolate-
workspaces (which I never got to work properly anyways) and after a
reboot everything was fine again.

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https://bugs.launchpad.net/bugs/1798792

Title:
  Gnome is very unstable, search not working, icons on dock disappearing

Status in gnome-shell package in Ubuntu:
  New

Bug description:
  Just after an upgrade to 18.10 (from 18.04).

  The icons on the dock disappear spontaneously, becoming blank.

  When searching for apps (which becomes even more important because of
  the previous bug), it hangs and no apps are shown whatsoever)

  ProblemType: Bug
  DistroRelease: Ubuntu 18.10
  Package: gnome-shell 3.30.1-2ubuntu1
  ProcVersionSignature: Ubuntu 4.18.0-10.11-generic 4.18.12
  Uname: Linux 4.18.0-10-generic x86_64
  ApportVersion: 2.20.10-0ubuntu13
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Fri Oct 19 11:55:13 2018
  DisplayManager: gdm3
  InstallationDate: Installed on 2018-07-30 (80 days ago)
  InstallationMedia: Ubuntu 18.04.1 LTS "Bionic Beaver" - Release amd64 
(20180725)
  SourcePackage: gnome-shell
  UpgradeStatus: Upgraded to cosmic on 2018-10-19 (0 days ago)

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