I am having the same problem. A few days ago I upgraded my computer from Ubuntu 
19.10 to 20.04. Normally I was starting the MySql server manually. It started 
working automatically with the update.
When I put the computer to sleep mode and turn it back on, the authentication 
window for the MySql server is opening at the upper left corner and is not 
closing in any way.
The thing that catches my attention here is that when I click on the window 
that does not close, the application under the window detects the click. 
However, the cancel button and the password text box is not performing their 
functions even though they sense the clicks correctly.
Notice: Restarting the shell closes the window.

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https://bugs.launchpad.net/bugs/1824874

Title:
  undismissable, unclickable authentication dialog left on screen (top-
  left corner) after policykit authentication [pushModal: invocation of
  begin_modal failed]

Status in gnome-shell package in Ubuntu:
  Confirmed

Bug description:
  In disco, when policykit prompted me for a password in order for
  update-manager to dispatch instructions to aptdaemon to perform
  package updates, the password dialog remained on the screen after I
  clicked 'authenticate'.

  The window is not clickable, it appears not to even be a window -
  mouse presses are received by the window underneath.  The exception is
  that the 'cancel' button is active and receives mouse events - but
  clicking it does nothing.

  This may be a gnome-shell issue rather than policykit.

  ProblemType: Bug
  DistroRelease: Ubuntu 19.04
  Package: policykit-1 0.105-25
  ProcVersionSignature: Ubuntu 5.0.0-8.9-generic 5.0.1
  Uname: Linux 5.0.0-8-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
  ApportVersion: 2.20.10-0ubuntu27
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Mon Apr 15 13:14:33 2019
  InstallationDate: Installed on 2010-09-24 (3125 days ago)
  InstallationMedia: Ubuntu 10.04.1 LTS "Lucid Lynx" - Release amd64 
(20100816.1)
  SourcePackage: policykit-1
  UpgradeStatus: Upgraded to disco on 2019-04-11 (3 days ago)

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