I know this is Ubuntu bug reporting tool, but I have the same problem on 
Fedora. I didn't find this bug reported on Fedora (I'll report it), but I'd 
like to add some observations for you, so maybe someone will be able to solve 
this annoying issue.
I use Yubikey to login to my Gnome desktop. Everything works fine until I run 
any program as root (e.g. virt-manager, disks). Then I'm asked to touch my 
Yubikey to authorize and to run the program as root. So far good.
But then I lock the screen (or it locks itself after 5 minutes). When I unlock 
the screen by touching the Yubikey I see the annoyuing dialog with message 
"System policy prevents management of the local virtualized systems".
I've checked /etc/pam.d/polkit-1 if it uses Yubikey for authentication

#%PAM-1.0
auth       include      system-auth
account    include      system-auth
password   include      system-auth
session    include      system-auth

and /etc/pam.d/system-auth contains

auth        required                                     pam_env.so
auth        required                                     pam_faildelay.so 
delay=2000000
auth        sufficient                                   pam_fprintd.so
auth        sufficient                                   pam_u2f.so debug=1
auth        sufficient                                   pam_yubico.so id=1 
debug=1
...

Login and other PAM modules use system-auth config as well. So I'd
expect that polkit should work with this. But it doesn't. Maybe it need
more configuration in other pam sections (account, password, session).
I'm not PAM expert.

I hope this will help someone to find a fix.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-shell in Ubuntu.
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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