I just tried some experiments with pam_yubico in my distro.

Case 1 (OK):

- Run `systemctl restart some-service` (for example: `systemctl restart 
libvirtd`).
- Go sleep or lock screen (press Super+L).
- Wakeup and login again.

==> There are no any popups.

Case 2 (Bug):

- Connect Yubikey.
- Edit /etc/pam.d configuration files (for example: common-session in Ubuntu or 
system-auth in other distro) and describe a long-running `auth sufficient ...` 
module (for example: pam_yubico.so).
- Run `systemctl restart some-service` (for example: `systemctl restart 
libvirtd`), interact with the Yubikey.
- Go sleep or lock screen (press Super+L).
- Wakeup and login again.

==> An undismissable popup says that authentication is required to
restart libvirtd (or any other service).

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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]

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