Current workaround appears to be:
1. "Un"-maximize the window (aka "restore" the window)
2. Interact with the window at least once.
3. Maximize the window again.

This appears to somehow work around this focus "click through" issue.

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https://bugs.launchpad.net/bugs/2026194

Title:
  When clicking on some maximized or tiled windows, focus on roughly the
  lower quarter falls to the window behind

Status in gnome-shell package in Ubuntu:
  New

Bug description:
  Initially I thought this was an issue with IntelliJ and filed a bug there:
  
https://youtrack.jetbrains.com/issue/IDEA-323780/Maximizing-the-the-window-sometimes-causes-clicks-on-a-lower-fraction-to-pass-through-to-the-window-behind

  But when I had the same issue with GIMP, I realized it's an Ubuntu or
  GNOME issue instead. I am assuming this is a gnome-shell problem.

  
  Every once in a while, when I maximize or tile (Win+Right) the IntelliJ 
window, a bottom fraction of the window (somewhere around a quarter) becomes 
impossible to interact with, with the mouse. Clicking in that lower area will 
give focus to the thing behind IntelliJ, and if it's a window, raise it to the 
foreground. if I restore the window so that it is not maximized, the entire 
window is interactive with the mouse once again.

  This also happened with GIMP.

  
  The attached "Screencast" is a recording. I had to crop it to hide personal 
information. The attached screenshot shows the state of my screen so you have 
context, with a bright green color used to replace personal information.

  For the first 10s of the recording, I simply moused over to show how
  the cursor changes around a quarter from the bottom of the screen.

  For the next 10s, I left click, then move, then left click, then move,
  until focus changes to Sublime, the window behind IntelliJ.

  For the remainder of the video I show that right-clicking and mousing
  over works fine on the top three quarters, until I reach the bottom
  again, and then the right click is sent to Sublime.

  
  Ubuntu 23.04
  gnome-shell version 44.2-0ubuntu1

  ProblemType: Bug
  DistroRelease: Ubuntu 23.04
  Package: gnome-shell 44.2-0ubuntu1
  ProcVersionSignature: Ubuntu 6.2.0-24.24-generic 6.2.12
  Uname: Linux 6.2.0-24-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
  ApportVersion: 2.26.1-0ubuntu2
  Architecture: amd64
  CasperMD5CheckResult: pass
  CurrentDesktop: ubuntu:GNOME
  Date: Wed Jul  5 12:05:46 2023
  DisplayManager: gdm3
  InstallationDate: Installed on 2022-09-19 (289 days ago)
  InstallationMedia: Ubuntu 22.04.1 LTS "Jammy Jellyfish" - Release amd64 
(20220809.1)
  ProcEnviron:
   LANG=en_US.UTF-8
   PATH=(custom, no user)
   SHELL=/usr/bin/zsh
   TERM=screen-256color
   XDG_RUNTIME_DIR=<set>
  RelatedPackageVersions: mutter-common 44.2-0ubuntu1
  SourcePackage: gnome-shell
  UpgradeStatus: No upgrade log present (probably fresh install)

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