Tested on physical hardware with 19.04. The issue is still present but
the viaul manifestaton is slightly different. Rather than black flickers
it's more of a shading effect that flickers on and off with mouse
movement. It can also be caused by enabling the option to extent the
magnified contents beyond the bounds of the desktop.

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https://bugs.launchpad.net/bugs/1831140

Title:
  GNOME Magnifier Flickering when using none-full screen  modes

Status in gnome-shell package in Ubuntu:
  New

Bug description:
  When using the GNOME magnifier (Zoom) feature the magnified display
  flickers when used in any of the following modes: Left, Right, Top or
  Bottom screen part. This occures when the mouse moves towards the edge
  directly opossite to the magnified view.

  To reproduce:
  * Open GNOME Control Centre.
  * Go to Universal Access.
  * Click on Zoom.
  * Enable Zoom
  * Selct either Top, Bottom, Left or Right from the screen part drop down list.
  * Move the mouse cursor to the opossite edge of the screen to that where the 
magnified view is located.

  I have tested on multiple systems running Ubuntu 18.04. I am yet to
  test with 19.04.

  I use this feature to allow me to use two monitors with one showing a
  magnified view the other showing a normal view.

  Happy to provide additional details.

  ProblemType: Bug
  DistroRelease: Ubuntu 18.04
  Package: gnome-shell 3.28.3+git20190124-0ubuntu18.04.2
  ProcVersionSignature: Ubuntu 4.18.0-21.22~18.04.1-generic 4.18.20
  Uname: Linux 4.18.0-21-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
  ApportVersion: 2.20.9-0ubuntu7.6
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Thu May 30 19:14:43 2019
  DisplayManager: gdm3
  ExecutablePath: /usr/bin/gnome-shell
  InstallationDate: Installed on 2019-03-12 (78 days ago)
  InstallationMedia: Ubuntu 18.04.1 LTS "Bionic Beaver" - Release amd64 
(20180725)
  ProcEnviron:
   LANGUAGE=en_GB:en
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_GB.UTF-8
   SHELL=/bin/bash
  SourcePackage: gnome-shell
  UpgradeStatus: No upgrade log present (probably fresh install)

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